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Fix to address deferred save of TermConcept when code system version changes prior to save.

This commit is contained in:
ianmarshall 2020-06-30 15:07:14 -04:00
parent 2cdef055aa
commit 0788e79d51
6 changed files with 81 additions and 20 deletions
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5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoObservationDstu3.java
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -32,16 +31,12 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.dstu3.model.Observation;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletResponse;
import java.util.Date;
public class FhirResourceDaoObservationDstu3 extends BaseHapiFhirResourceDaoObservation<Observation> {
@Autowired
ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
@Override
public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoObservationR4.java
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.r4;
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -32,7 +31,6 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Observation;
import org.springframework.beans.factory.annotation.Autowired;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
@ -46,9 +44,6 @@ public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDaoObserva
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
@Override
public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoObservationR5.java
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.r5;
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -32,16 +31,12 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.Observation;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletResponse;
import java.util.Date;
public class FhirResourceDaoObservationR5 extends BaseHapiFhirResourceDaoObservation<Observation> {
@Autowired
ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
@Override
public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
@ -62,7 +63,8 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
@Autowired
protected ITermCodeSystemDao myCodeSystemDao;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Autowired protected PlatformTransactionManager myTransactionMgr;
private boolean myProcessDeferred = true;
private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
@ -142,7 +144,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
ourLog.info("Saving {} deferred concepts...", count);
while (codeCount < count && myDeferredConcepts.size() > 0) {
TermConcept next = myDeferredConcepts.remove(0);
if(myCodeSystemVersionDao.findById(next.getCodeSystemVersion().getPid()).isPresent()) {
codeCount += myCodeSystemStorageSvc.saveConcept(next);
} else {
ourLog.warn("Unable to save deferred TermConcept {} because Code System {} version PID {} is no longer valid. Code system may have since been updated.",
next.getCode(), next.getCodeSystemVersion().getCodeSystemDisplayName(), next.getCodeSystemVersion().getPid());
}
}
if (codeCount > 0) {

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PersistObservationIndexedSearchParamLastNR4IT.java
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@ -203,9 +203,6 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
List<ObservationJson> observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(100, observationDocuments.size());
//List<CodeJson> codeDocuments = elasticsearchSvc.queryAllIndexedObservationCodesForTest();
//assertEquals(2, codeDocuments.size());
// Check that all observations were indexed.
searchParameterMap = new SearchParameterMap();
searchParameterMap.add(Observation.SP_SUBJECT, multiSubjectParams);

72
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcTest.java Normal file
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@ -0,0 +1,72 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.Test;
import java.io.IOException;
import static org.junit.Assert.assertEquals;
public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
private void createCodeSystemWithMoreThan100Concepts() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
cs.getConcepts().add(parentA);
for (int i = 0; i < 450; i++) {
TermConcept childI = new TermConcept(cs, "subCodeA" + i).setDisplay("Sub-code A" + i);
parentA.addChild(childI, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
}
TermConcept parentB = new TermConcept(cs, "codeB").setDisplay("CodeB");
cs.getConcepts().add(parentB);
for (int i = 0; i < 450; i++) {
TermConcept childI = new TermConcept(cs, "subCodeB" + i).setDisplay("Sub-code B" + i);
parentB.addChild(childI, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
}
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
}
@Test
public void testStoreNewCodeSystemVersionForExistingCodeSystem() throws IOException {
CodeSystem upload = loadResourceFromClasspath(CodeSystem.class, "/bundles-009_test.json");
ResourceTable codeSystemResourceEntity = (ResourceTable)myCodeSystemDao.create(upload, mySrd).getEntity();
runInTransaction(() -> {
myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity);
});
myTerminologyDeferredStorageSvc.setProcessDeferred(true);
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
assertEquals(124, myTermConceptDao.count());
}
}