Merge pull request #1960 from jamesagnew/im_20200630_code_system_load

Accidentally merged pull request before pushing changes from code review

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java

@@ -146,7 +146,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 		while (codeCount < count && myDeferredConcepts.size() > 0) {
 			TermConcept next = myDeferredConcepts.remove(0);
 			if(myCodeSystemVersionDao.findById(next.getCodeSystemVersion().getPid()).isPresent()) {
-         	codeCount += myCodeSystemStorageSvc.saveConcept(next);
+				try {
+					codeCount += myCodeSystemStorageSvc.saveConcept(next);
+				} catch (Exception theE) {
+					ourLog.error("Exception thrown when attempting to save TermConcept {} in Code System {}",
+						next.getCode(), next.getCodeSystemVersion().getCodeSystemDisplayName(), theE);
+				}
 			} 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 				ourLog.warn("Unable to save deferred TermConcept {} because Code System {} version PID {} is no longer valid.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());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcTest.java

@@ -12,6 +12,28 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
 
 	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() {
 		CodeSystem codeSystem = new CodeSystem();
 		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());
-	}
-
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImplTest.java

@@ -21,7 +21,6 @@ import static org.mockito.Mockito.*;
 @RunWith(MockitoJUnitRunner.class)
 public class TermDeferredStorageSvcImplTest {
 
-
 	@Mock
 	private PlatformTransactionManager myTxManager;
 	@Mock
@@ -69,6 +68,7 @@ public class TermDeferredStorageSvcImplTest {
 		concept.setCode("CODE_A");
 
 		TermCodeSystemVersion myTermCodeSystemVersion = new TermCodeSystemVersion();
+		myTermCodeSystemVersion.setId(1L);
 		concept.setCodeSystemVersion(myTermCodeSystemVersion);
 
 		TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
@@ -76,15 +76,45 @@ public class TermDeferredStorageSvcImplTest {
 		svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
 		svc.setDaoConfigForUnitTest(new DaoConfig());
 
+		when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.empty());
 		svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
 		svc.setProcessDeferred(true);
 		svc.addConceptToStorageQueue(concept);
 		svc.saveDeferred();
+
 		verify(myTermConceptStorageSvc, times(0)).saveConcept(same(concept));
 		verifyNoMoreInteractions(myTermConceptStorageSvc);
 
 	}
 
+	@Test
+	public void testSaveDeferred_Concept_Exception() {
+		// There is a small
+		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());
+
+		// Simulate the case where an exception is thrown despite a valid code system version.
+		when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.of(myTermCodeSystemVersion));
+		when(myTermConceptStorageSvc.saveConcept(concept)).thenThrow(new RuntimeException("Foreign Constraint Violation"));
+		svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
+		svc.setProcessDeferred(true);
+		svc.addConceptToStorageQueue(concept);
+		svc.saveDeferred();
+
+		verify(myTermConceptStorageSvc, times(1)).saveConcept(same(concept));
+		verifyNoMoreInteractions(myTermConceptStorageSvc);
+
+	}
+
 	@Test
 	public void testSaveDeferred_ConceptParentChildLink_ConceptsMissing() {
 		TermConceptParentChildLink conceptLink = new TermConceptParentChildLink();