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Changes from code review

This commit is contained in:
ianmarshall 2020-07-03 13:08:11 -04:00
parent 46abdfafe0
commit 4e5ca2ee15
3 changed files with 29 additions and 23 deletions
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7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
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@ -50,6 +50,7 @@ import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate; import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct; import javax.annotation.PostConstruct;
import java.sql.SQLException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.List; import java.util.List;
@ -145,10 +146,10 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
ourLog.info("Saving {} deferred concepts...", count); ourLog.info("Saving {} deferred concepts...", count);
while (codeCount < count && myDeferredConcepts.size() > 0) { while (codeCount < count && myDeferredConcepts.size() > 0) {
TermConcept next = myDeferredConcepts.remove(0); TermConcept next = myDeferredConcepts.remove(0);
if(myCodeSystemVersionDao.findById(next.getCodeSystemVersion().getPid()).isPresent()) { try {
codeCount += myCodeSystemStorageSvc.saveConcept(next); codeCount += myCodeSystemStorageSvc.saveConcept(next);
} else { } catch (Exception theE) {
ourLog.warn("Unable to save deferred TermConcept {} because Code System {} version PID {} is no longer valid. Code system may have since been replaced.", ourLog.warn("Unable to save deferred TermConcept {}, possibly because Code System {} version PID {} may have since been replaced.",
next.getCode(), next.getCodeSystemVersion().getCodeSystemDisplayName(), next.getCodeSystemVersion().getPid()); next.getCode(), next.getCodeSystemVersion().getCodeSystemDisplayName(), next.getCodeSystemVersion().getPid());
} }
} }

37
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcTest.java
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@ -12,6 +12,28 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system"; public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
@Test
public void testStoreNewCodeSystemVersionForExistingCodeSystem() {
CodeSystem upload = createCodeSystemWithMoreThan100Concepts();
// Create CodeSystem resource
ResourceTable codeSystemResourceEntity = (ResourceTable)myCodeSystemDao.create(upload, mySrd).getEntity();
// Update the CodeSystem resource
runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity));
/*
Because there are more than 100 concepts in the code system, the first 100 will be persisted immediately and
the remaining 25 concepts will be queued up for "deferred save".
As the CodeSystem was persisted twice, the extra 25 term concepts will be queued twice, each with a different
CodeSystem version PID. Only one set of the term concepts should be persisted (i.e. 125 term concepts in total).
*/
myTerminologyDeferredStorageSvc.setProcessDeferred(true);
myTerminologyDeferredStorageSvc.saveDeferred();
assertEquals(125, myTermConceptDao.count());
}
private CodeSystem createCodeSystemWithMoreThan100Concepts() { private CodeSystem createCodeSystemWithMoreThan100Concepts() {
CodeSystem codeSystem = new CodeSystem(); CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM); codeSystem.setUrl(URL_MY_CODE_SYSTEM);
@ -25,20 +47,5 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
} }
@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());
}
} }

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImplTest.java
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@ -13,15 +13,12 @@ import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner; import org.mockito.junit.MockitoJUnitRunner;
import org.springframework.transaction.PlatformTransactionManager; import org.springframework.transaction.PlatformTransactionManager;
import java.util.Optional;
import static org.mockito.ArgumentMatchers.same; import static org.mockito.ArgumentMatchers.same;
import static org.mockito.Mockito.*; import static org.mockito.Mockito.*;
@RunWith(MockitoJUnitRunner.class) @RunWith(MockitoJUnitRunner.class)
public class TermDeferredStorageSvcImplTest { public class TermDeferredStorageSvcImplTest {
@Mock @Mock
private PlatformTransactionManager myTxManager; private PlatformTransactionManager myTxManager;
@Mock @Mock
@ -53,7 +50,6 @@ public class TermDeferredStorageSvcImplTest {
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc); svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
svc.setDaoConfigForUnitTest(new DaoConfig()); svc.setDaoConfigForUnitTest(new DaoConfig());
when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.of(myTermCodeSystemVersion));
svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao); svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
svc.setProcessDeferred(true); svc.setProcessDeferred(true);
svc.addConceptToStorageQueue(concept); svc.addConceptToStorageQueue(concept);
@ -76,11 +72,13 @@ public class TermDeferredStorageSvcImplTest {
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc); svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
svc.setDaoConfigForUnitTest(new DaoConfig()); svc.setDaoConfigForUnitTest(new DaoConfig());
when(myTermConceptStorageSvc.saveConcept(concept)).thenThrow(new RuntimeException("Foreign Constraint Violation"));
svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao); svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
svc.setProcessDeferred(true); svc.setProcessDeferred(true);
svc.addConceptToStorageQueue(concept); svc.addConceptToStorageQueue(concept);
svc.saveDeferred(); svc.saveDeferred();
verify(myTermConceptStorageSvc, times(0)).saveConcept(same(concept));
verify(myTermConceptStorageSvc, times(1)).saveConcept(same(concept));
verifyNoMoreInteractions(myTermConceptStorageSvc); verifyNoMoreInteractions(myTermConceptStorageSvc);
} }