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Merge pull request #1958 from jamesagnew/im_20200630_code_system_load 

Im 20200630 code system load
This commit is contained in:
IanMMarshall 2020-07-03 13:06:42 -04:00 committed by GitHub
parent aa1e46fdb0 46abdfafe0
commit 0e885064ce
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7 changed files with 94 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) {

15
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;
@ -62,6 +63,8 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
@Autowired
protected ITermCodeSystemDao myCodeSystemDao;
@Autowired
protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
private boolean myProcessDeferred = true;
private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
@ -142,7 +145,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
ourLog.info("Saving {} deferred concepts...", count);
while (codeCount < count && myDeferredConcepts.size() > 0) {
TermConcept next = myDeferredConcepts.remove(0);
codeCount += myCodeSystemStorageSvc.saveConcept(next);
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 replaced.",
next.getCode(), next.getCodeSystemVersion().getCodeSystemDisplayName(), next.getCodeSystemVersion().getPid());
}
}
if (codeCount > 0) {
@ -340,4 +348,9 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
void setConceptDaoForUnitTest(ITermConceptDao theConceptDao) {
myConceptDao = theConceptDao;
}
@VisibleForTesting
void setCodeSystemVersionDaoForUnitTest(ITermCodeSystemVersionDao theCodeSystemVersionDao) {
myCodeSystemVersionDao = theCodeSystemVersionDao;
}
}

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);

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcTest.java Normal file
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@ -0,0 +1,44 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.junit.Test;
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 CodeSystem createCodeSystemWithMoreThan100Concepts() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
for (int i = 0; i < 125; i++) {
codeSystem.addConcept(new CodeSystem.ConceptDefinitionComponent(new CodeType("codeA " + i)));
}
return codeSystem;
}
@Test
public void testStoreNewCodeSystemVersionForExistingCodeSystem() {
CodeSystem upload = createCodeSystemWithMoreThan100Concepts();
ResourceTable codeSystemResourceEntity = (ResourceTable)myCodeSystemDao.create(upload, mySrd).getEntity();
runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity));
myTerminologyDeferredStorageSvc.setProcessDeferred(true);
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
assertEquals(125, myTermConceptDao.count());
}
}

37
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImplTest.java
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@ -1,7 +1,9 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
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.term.api.ITermCodeSystemStorageSvc;
@ -11,6 +13,8 @@ import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import org.springframework.transaction.PlatformTransactionManager;
import java.util.Optional;
import static org.mockito.ArgumentMatchers.same;
import static org.mockito.Mockito.*;
@ -24,6 +28,8 @@ public class TermDeferredStorageSvcImplTest {
private ITermCodeSystemStorageSvc myTermConceptStorageSvc;
@Mock
private ITermConceptDao myConceptDao;
@Mock
private ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
@Test
public void testSaveDeferredWithExecutionSuspended() {
@ -38,16 +44,45 @@ public class TermDeferredStorageSvcImplTest {
TermConcept concept = new TermConcept();
concept.setCode("CODE_A");
TermCodeSystemVersion myTermCodeSystemVersion = new TermCodeSystemVersion();
myTermCodeSystemVersion.setId(1L);
concept.setCodeSystemVersion(myTermCodeSystemVersion);
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
svc.setTransactionManagerForUnitTest(myTxManager);
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
svc.setDaoConfigForUnitTest(new DaoConfig());
when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.of(myTermCodeSystemVersion));
svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
svc.setProcessDeferred(true);
svc.addConceptToStorageQueue(concept);
svc.saveDeferred();
verify(myTermConceptStorageSvc, times(1)).saveConcept(same(concept));
verifyNoMoreInteractions(myTermConceptStorageSvc);
}
@Test
public void testSaveDeferred_Concept_StaleCodeSystemVersion() {
TermConcept concept = new TermConcept();
concept.setCode("CODE_A");
TermCodeSystemVersion myTermCodeSystemVersion = new TermCodeSystemVersion();
concept.setCodeSystemVersion(myTermCodeSystemVersion);
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
svc.setTransactionManagerForUnitTest(myTxManager);
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
svc.setDaoConfigForUnitTest(new DaoConfig());
svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
svc.setProcessDeferred(true);
svc.addConceptToStorageQueue(concept);
svc.saveDeferred();
verify(myTermConceptStorageSvc, times(0)).saveConcept(same(concept));
verifyNoMoreInteractions(myTermConceptStorageSvc);
}
@Test