Fix to address deferred save of TermConcept when code system version changes prior to save.
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.dstu3;
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*/
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
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import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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@ -32,16 +31,12 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.dstu3.model.Observation;
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import org.springframework.beans.factory.annotation.Autowired;
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import javax.servlet.http.HttpServletResponse;
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import java.util.Date;
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public class FhirResourceDaoObservationDstu3 extends BaseHapiFhirResourceDaoObservation<Observation> {
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@Autowired
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ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
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@Override
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public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.r4;
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*/
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
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import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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@ -32,7 +31,6 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.Observation;
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import org.springframework.beans.factory.annotation.Autowired;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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@ -46,9 +44,6 @@ public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDaoObserva
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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@Autowired
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ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
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@Override
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public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao.r5;
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*/
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
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import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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@ -32,16 +31,12 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r5.model.Observation;
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import org.springframework.beans.factory.annotation.Autowired;
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import javax.servlet.http.HttpServletResponse;
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import java.util.Date;
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public class FhirResourceDaoObservationR5 extends BaseHapiFhirResourceDaoObservation<Observation> {
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@Autowired
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ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
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@Override
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public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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@ -62,7 +63,8 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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@Autowired
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protected ITermCodeSystemDao myCodeSystemDao;
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@Autowired
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protected PlatformTransactionManager myTransactionMgr;
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protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
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@Autowired protected PlatformTransactionManager myTransactionMgr;
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private boolean myProcessDeferred = true;
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private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
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private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
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@ -142,7 +144,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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ourLog.info("Saving {} deferred concepts...", count);
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while (codeCount < count && myDeferredConcepts.size() > 0) {
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TermConcept next = myDeferredConcepts.remove(0);
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codeCount += myCodeSystemStorageSvc.saveConcept(next);
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if(myCodeSystemVersionDao.findById(next.getCodeSystemVersion().getPid()).isPresent()) {
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codeCount += myCodeSystemStorageSvc.saveConcept(next);
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} else {
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ourLog.warn("Unable to save deferred TermConcept {} because Code System {} version PID {} is no longer valid. Code system may have since been updated.",
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next.getCode(), next.getCodeSystemVersion().getCodeSystemDisplayName(), next.getCodeSystemVersion().getPid());
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}
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}
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if (codeCount > 0) {
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@ -203,9 +203,6 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
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List<ObservationJson> observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
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assertEquals(100, observationDocuments.size());
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//List<CodeJson> codeDocuments = elasticsearchSvc.queryAllIndexedObservationCodesForTest();
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//assertEquals(2, codeDocuments.size());
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// Check that all observations were indexed.
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searchParameterMap = new SearchParameterMap();
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searchParameterMap.add(Observation.SP_SUBJECT, multiSubjectParams);
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@ -0,0 +1,72 @@
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package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.junit.Test;
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import java.io.IOException;
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import static org.junit.Assert.assertEquals;
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public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
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public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
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private void createCodeSystemWithMoreThan100Concepts() {
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CodeSystem codeSystem = new CodeSystem();
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codeSystem.setUrl(URL_MY_CODE_SYSTEM);
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codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
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IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
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ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
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TermCodeSystemVersion cs = new TermCodeSystemVersion();
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cs.setResource(table);
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TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
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cs.getConcepts().add(parentA);
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for (int i = 0; i < 450; i++) {
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TermConcept childI = new TermConcept(cs, "subCodeA" + i).setDisplay("Sub-code A" + i);
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parentA.addChild(childI, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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}
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TermConcept parentB = new TermConcept(cs, "codeB").setDisplay("CodeB");
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cs.getConcepts().add(parentB);
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for (int i = 0; i < 450; i++) {
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TermConcept childI = new TermConcept(cs, "subCodeB" + i).setDisplay("Sub-code B" + i);
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parentB.addChild(childI, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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}
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myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
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}
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@Test
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public void testStoreNewCodeSystemVersionForExistingCodeSystem() throws IOException {
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CodeSystem upload = loadResourceFromClasspath(CodeSystem.class, "/bundles-009_test.json");
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ResourceTable codeSystemResourceEntity = (ResourceTable)myCodeSystemDao.create(upload, mySrd).getEntity();
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runInTransaction(() -> {
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myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity);
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});
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myTerminologyDeferredStorageSvc.setProcessDeferred(true);
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myTerminologyDeferredStorageSvc.saveDeferred();
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myTerminologyDeferredStorageSvc.saveDeferred();
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assertEquals(124, myTermConceptDao.count());
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}
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}
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