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Test fixes

This commit is contained in:
James Agnew 2019-09-19 14:42:27 -04:00
parent a5a0fca065
commit 47805bceff
8 changed files with 57 additions and 47 deletions
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62
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -30,7 +30,6 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -75,7 +74,6 @@ import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
@ -1642,7 +1640,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion) {
public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
ourLog.info("Storing code system");
ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
@ -1669,24 +1667,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
* Do the upload
*/
TermCodeSystem codeSystem = getCodeSystem(theSystemUri);
if (codeSystem == null) {
codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid);
if (codeSystem == null) {
codeSystem = new TermCodeSystem();
}
codeSystem.setResource(theCodeSystemVersion.getResource());
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
}
codeSystem.setCodeSystemUri(theSystemUri);
codeSystem.setName(theSystemName);
codeSystem = myCodeSystemDao.save(codeSystem);
TermCodeSystem codeSystem = getOrCreateTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theCodeSystemResourceTable);
theCodeSystemVersion.setCodeSystem(codeSystem);
@ -1737,6 +1718,29 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
@Nonnull
private TermCodeSystem getOrCreateTermCodeSystem(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
TermCodeSystem codeSystem = getCodeSystem(theSystemUri);
if (codeSystem == null) {
codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid);
if (codeSystem == null) {
codeSystem = new TermCodeSystem();
}
codeSystem.setResource(theCodeSystemResourceTable);
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemResourceTable.getId())) {
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
}
codeSystem.setCodeSystemUri(theSystemUri);
codeSystem.setName(theSystemName);
codeSystem = myCodeSystemDao.save(codeSystem);
return codeSystem;
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequest, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
@ -1751,7 +1755,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
populateCodeSystemVersionProperties(theCodeSystemVersion, theCodeSystemResource, resource);
storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemResource.getVersion(), theCodeSystemVersion);
storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemResource.getVersion(), theCodeSystemVersion, resource);
myDeferredConceptMaps.addAll(theConceptMaps);
myDeferredValueSets.addAll(theValueSets);
@ -1773,23 +1777,29 @@ 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());
// If this is a not-present codesystem, we don't want to store a new version if one
// already exists, since that will wipe out the existing concepts
Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
/*
* If this is a not-present codesystem, we don't want to store a new version if one
* already exists, since that will wipe out the existing concepts. We do create or update
* the TermCodeSystem table though, since that allows the DB to reject changes
* that would result in duplicate CodeSysten.url values.
*/
if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theCodeSystem.getUrl());
if (codeSystem != null) {
getOrCreateTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theResourceEntity);
return;
}
}
Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
TermCodeSystemVersion persCs = new TermCodeSystemVersion();
populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
persCs.getConcepts().addAll(toPersistedConcepts(theCodeSystem.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs);
storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs, theResourceEntity);
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
View File

@ -84,7 +84,7 @@ public interface IHapiTerminologySvc {
*/
void setProcessDeferred(boolean theProcessDeferred);
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion);
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
/**
* @return Returns the ID of the created/updated code system

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
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@ -103,7 +103,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
parentC.addChild(childCA, RelationshipTypeEnum.ISA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}
@ -134,7 +134,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
parentB.addChild(childI, RelationshipTypeEnum.ISA);
}
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
return codeSystem;
}
@ -170,7 +170,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
dogs.addChild(beagle, RelationshipTypeEnum.ISA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME", "SYSTEM VERSION" , cs, table);
return codeSystem;
}
@ -689,7 +689,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
cs.setResource(table);
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs, table);
StringType code = new StringType("ParentA");
StringType system = new StringType("http://snomed.info/sct");

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
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@ -101,7 +101,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
parentC.addChild(childCA, RelationshipTypeEnum.ISA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}
@ -137,7 +137,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
dogs.addChild(beagle, RelationshipTypeEnum.ISA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}
@ -168,7 +168,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
parentB.addChild(childI, RelationshipTypeEnum.ISA);
}
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}
@ -481,7 +481,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
concept = new TermConcept(cs, "LA9999-7");
cs.getConcepts().add(concept);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
ValueSet valueSet = new ValueSet();
valueSet.setUrl(URL_MY_VALUE_SET);
@ -808,7 +808,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
cs.setResource(table);
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs, table);
StringType code = new StringType("ParentA");
StringType system = new StringType("http://snomed.info/sct");

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -187,7 +187,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
code.addPropertyString("HELLO", "12345-2");
cs.getConcepts().add(code);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
});
}
@ -886,7 +886,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs);
theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
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@ -876,7 +876,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs);
theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
return codeSystem;
}

14
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -98,7 +98,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return id;
}
@ -117,7 +117,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
TermConcept parentA = new TermConcept(cs, "CS2");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL_2, "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL_2, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
return id;
}
@ -184,7 +184,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
code2.getDisplay());
cs.getConcepts().add(code4);
myTermSvc.storeNewCodeSystemVersion(table.getId(), LOINC_URI, "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), LOINC_URI, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
});
}
@ -200,7 +200,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
// Update
cs = new TermCodeSystemVersion();
@ -209,7 +209,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
id = myCodeSystemDao.update(codeSystem, null, true, true, mySrd).getId().toUnqualified();
table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
cs.setResource(table);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
// Try to update to a different resource
codeSystem = new CodeSystem();
@ -1327,7 +1327,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
child.addChild(parent, RelationshipTypeEnum.ISA);
try {
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION" , cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
fail();
} catch (InvalidRequestException e) {
assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
@ -1452,7 +1452,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
runInTransaction(()->{
ResourceTable resTable = myEntityManager.find(ResourceTable.class, csId.getIdPartAsLong());
version.setResource(resTable);
myTermSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", "SYSTEM VERSION" , version);
myTermSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", "SYSTEM VERSION" , version, resTable);
});
org.hl7.fhir.dstu3.model.ValueSet vs = new org.hl7.fhir.dstu3.model.ValueSet();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
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@ -116,7 +116,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return id;
}