Changes to enable request delete of specific Code System version.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -25,7 +25,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@@ -67,6 +69,8 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	private FhirContext myFhirContext;
@@ -148,13 +152,9 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
 		super.preDelete(theResourceToDelete, theEntityToDelete);
 
-		String codeSystemUrl = theResourceToDelete.getUrl();
+		HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
-		if (isNotBlank(codeSystemUrl)) {
+			theResourceToDelete.getVersion());
-			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
+
-			if (persCs != null) {
-				myTermDeferredStorageSvc.deleteCodeSystem(persCs);
-			}
-		}
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java

@@ -25,7 +25,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@@ -61,6 +63,8 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
@@ -146,13 +150,9 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
 		super.preDelete(theResourceToDelete, theEntityToDelete);
 
-		String codeSystemUrl = theResourceToDelete.getUrl();
+		HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
-		if (isNotBlank(codeSystemUrl)) {
+			theResourceToDelete.getVersion());
-			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
+
-			if (persCs != null) {
-				myTermDeferredStorageSvc.deleteCodeSystem(persCs);
-			}
-		}
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java

@@ -25,7 +25,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
@@ -65,6 +67,8 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	@Autowired
 	private ITermCodeSystemDao myCsDao;
 	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	@Autowired
 	private IValidationSupport myValidationSupport;
 	@Autowired
 	private FhirContext myFhirContext;
@@ -117,11 +121,11 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 			codeSystemVersion = theVersion.getValue();
 		}
 
-		ourLog.info("Looking up {} / {}, version {}", system, code, codeSystemVersion);
+		ourLog.debug("Looking up {} / {}, version {}", system, code, codeSystemVersion);
 
 		if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
 
-			ourLog.info("Code system {} is supported", system);
+			ourLog.debug("Code system {} is supported", system);
 			IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
 			if (retVal != null) {
 				return retVal;
@@ -148,13 +152,9 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
 		super.preDelete(theResourceToDelete, theEntityToDelete);
 
-		String codeSystemUrl = theResourceToDelete.getUrl();
+		HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
-		if (isNotBlank(codeSystemUrl)) {
+			theResourceToDelete.getVersion());
-			TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
+
-			if (persCs != null) {
-				myTermDeferredStorageSvc.deleteCodeSystem(persCs);
-			}
-		}
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java

@@ -58,7 +58,7 @@ public class TermCodeSystem implements Serializable {
 	@Column(name = "PID")
 	private Long myPid;
 	@OneToOne(fetch = FetchType.LAZY)
-	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
+	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = true, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
 	private ResourceTable myResource;
 	@Column(name = "RES_ID", insertable = false, updatable = false)
 	private Long myResourcePid;

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

@@ -231,6 +231,14 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		});
 	}
 
+	@Override
+	@Transactional(propagation = Propagation.NEVER)
+	public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
+		ourLog.info(" * Deleting code system version {}", theCodeSystemVersion.getPid());
+
+		deleteCodeSystemVersion(theCodeSystemVersion.getPid());
+	}
+
 	/**
 	 * Returns the number of saved concepts
 	 */
@@ -680,9 +688,9 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			if (codeSystem == null) {
 				codeSystem = new TermCodeSystem();
 			}
-			codeSystem.setResource(theCodeSystemResourceTable);
 		}
 
+		codeSystem.setResource(theCodeSystemResourceTable);
 		codeSystem.setCodeSystemUri(theSystemUri);
 		codeSystem.setName(theSystemName);
 		codeSystem = myCodeSystemDao.save(codeSystem);
@@ -692,15 +700,19 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 	private void validateCodeSystemVersionUpdate(TermCodeSystem theCodeSystem, String theSystemUri, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
 		// Check if CodeSystemVersion entity already exists.
 		TermCodeSystemVersion codeSystemVersionEntity;
-		String msg;
+		String msg = null;
 		if (theSystemVersionId == null) {
 			codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystem.getPid());
+			if (codeSystemVersionEntity != null) {
 				msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
-				theCodeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+					codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+			}
 		} else {
 			codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystem.getPid(), theSystemVersionId);
+			if (codeSystemVersionEntity != null) {
 				msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri,
-				theSystemVersionId, theCodeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+					theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
+			}
 		}
 		// Throw exception if the CodeSystemVersion is being duplicated.
 		if (codeSystemVersionEntity != null) {

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

@@ -26,6 +26,7 @@ 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;
+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.sched.HapiJob;
@@ -68,6 +69,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	protected PlatformTransactionManager myTransactionMgr;
 	private boolean myProcessDeferred = true;
 	private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
+	private List<TermCodeSystemVersion> myDefferedCodeSystemVersionsDeletions = Collections.synchronizedList(new ArrayList<>());
 	private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
 	private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
 	private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
@@ -115,6 +117,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 		myDefferedCodeSystemsDeletions.add(theCodeSystem);
 	}
 
+	@Override
+	@Transactional
+	public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
+		myDefferedCodeSystemVersionsDeletions.add(theCodeSystemVersion);
+	}
+
 	@Override
 	public void saveAllDeferred() {
 		while (!isStorageQueueEmpty()) {
@@ -266,6 +274,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	}
 
 	private void processDeferredCodeSystemDeletions() {
+
+		for (TermCodeSystemVersion next : myDefferedCodeSystemVersionsDeletions) {
+			myCodeSystemStorageSvc.deleteCodeSystemVersion(next);
+		}
+
+		myDefferedCodeSystemVersionsDeletions.clear();
 		for (TermCodeSystem next : myDefferedCodeSystemsDeletions) {
 			myCodeSystemStorageSvc.deleteCodeSystem(next);
 		}
@@ -300,7 +314,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	}
 
 	private boolean isDeferredCodeSystemDeletions() {
-		return !myDefferedCodeSystemsDeletions.isEmpty();
+		return !myDefferedCodeSystemsDeletions.isEmpty() || !myDefferedCodeSystemVersionsDeletions.isEmpty();
 	}
 
 	private boolean isDeferredConcepts() {

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

@@ -41,6 +41,8 @@ public interface ITermCodeSystemStorageSvc {
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 
+	void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
+
 	void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
 
 	/**

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term.api;
  */
 
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -54,6 +55,8 @@ public interface ITermDeferredStorageSvc {
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 
+	void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
+
 	/**
 	 * This is mostly here for unit tests - Saves any and all deferred concepts and links
 	 */

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

@@ -1,11 +1,19 @@
 package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeType;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
+
+import static org.junit.jupiter.api.Assertions.fail;
+
+
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
@@ -14,47 +22,123 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
 
 	@Test
 	public void testStoreNewCodeSystemVersionForExistingCodeSystemNoVersionId() {
-		CodeSystem upload = createCodeSystemWithMoreThan100Concepts();
+		CodeSystem firstUpload = createCodeSystemWithMoreThan100Concepts();
+		CodeSystem duplicateUpload = createCodeSystemWithMoreThan100Concepts();
 
-		// Create CodeSystem resource
+		testCreatingAndUpdatingCodeSystemEntity(firstUpload, duplicateUpload, 125, "Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/");
-		ResourceTable codeSystemResourceEntity = (ResourceTable) myCodeSystemDao.create(upload, mySrd).getEntity();
 
-		// Update the CodeSystem resource
+		runInTransaction(() -> {
-		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity));
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(URL_MY_CODE_SYSTEM);
 
-		/*
+			TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull( myTermCodeSystem.getPid());
-			Because there are more than 100 concepts in the code system, the first 100 will be persisted immediately and
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
-			the remaining 25 concepts will be queued up for "deferred save".
+			assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
-
+		});
-			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());
 	}
 
+
 	@Test
 	public void testStoreNewCodeSystemVersionForExistingCodeSystemVersionId() {
-		CodeSystem upload = createCodeSystemWithMoreThan100Concepts();
+		CodeSystem firstUpload = createCodeSystemWithMoreThan100Concepts();
-		upload.setVersion("1");
+		firstUpload.setVersion("1");
 
-		// Create CodeSystem resource
+		CodeSystem duplicateUpload = createCodeSystemWithMoreThan100Concepts();
-		ResourceTable codeSystemResourceEntity = (ResourceTable) myCodeSystemDao.create(upload, mySrd).getEntity();
+		duplicateUpload.setVersion("1");
 
-		// Update the CodeSystem resource
+		testCreatingAndUpdatingCodeSystemEntity(firstUpload, duplicateUpload, 125,"Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"1\", already have one with resource ID: CodeSystem/");
-		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(upload, codeSystemResourceEntity));
 
-		/*
+		runInTransaction(() -> {
-			Because there are more than 100 concepts in the code system, the first 100 will be persisted immediately and
+			assertEquals(1, myTermCodeSystemDao.count());
-			the remaining 25 concepts will be queued up for "deferred save".
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(URL_MY_CODE_SYSTEM);
+
+			TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion( myTermCodeSystem.getPid(), "1");
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
+			assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
+		});
+
+		// Now add a second version
+		firstUpload = createCodeSystemWithMoreThan100Concepts();
+		firstUpload.setVersion("2");
+
+		duplicateUpload = createCodeSystemWithMoreThan100Concepts();
+		duplicateUpload.setVersion("2");
+
+		testCreatingAndUpdatingCodeSystemEntity(firstUpload, duplicateUpload, 251,"Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"2\", already have one with resource ID: CodeSystem/");
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(URL_MY_CODE_SYSTEM);
+
+			TermCodeSystemVersion mySecondTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2");
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), mySecondTermCodeSystemVersion.getPid());
+			assertEquals(myTermCodeSystem.getResource().getId(), mySecondTermCodeSystemVersion.getResource().getId());
+		});
+
+	}
+
+	@Test
+	public void testDeleteCodeSystem() {
+		CodeSystem codeSystemToDelete = createSmallCodeSystem();
+
+		// Create CodeSystem resource and entity
+		ResourceTable codeSystemResourceEntity = (ResourceTable)myCodeSystemDao.create(codeSystemToDelete, mySrd).getEntity();
+		validateCodeSystemUpdates(10);
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+		});
+
+		// Attempt to delete
+		myCodeSystemDao.delete(codeSystemResourceEntity.getIdDt(), mySrd);
+		validateCodeSystemUpdates(0);
+
+		runInTransaction(() -> {
+			assertEquals(0, myTermCodeSystemDao.count());
+			assertEquals(0, myTermCodeSystemVersionDao.count());
+		});
+
+	}
+
+	@Test
+	public void testDeleteCodeSystemVersion() {
+		CodeSystem firstCodeSystemVersion = createSmallCodeSystem();
+		firstCodeSystemVersion.setVersion("1");
+
+		// Create first CodeSystem resource and entity
+		ResourceTable codeSystemResourceEntity = (ResourceTable)myCodeSystemDao.create(firstCodeSystemVersion, mySrd).getEntity();
+		validateCodeSystemUpdates(10);
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+		});
+
+		CodeSystem secondCodeSystemVersion = createSmallCodeSystem();
+		secondCodeSystemVersion.setVersion("2");
+
+		// Create CodeSystem resource and entity
+		myCodeSystemDao.create(secondCodeSystemVersion, mySrd);
+		validateCodeSystemUpdates(20);
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+		});
+
+		// Attempt to delete first version
+		myCodeSystemDao.delete(codeSystemResourceEntity.getIdDt(), mySrd);
+		validateCodeSystemUpdates(10);
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+		});
 
-			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() {
@@ -70,5 +154,56 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
 
 	}
 
+	private CodeSystem createSmallCodeSystem() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
+
+		for (int i = 0; i < 10; i++) {
+			codeSystem.addConcept(new CodeSystem.ConceptDefinitionComponent(new CodeType("codeA " + i)));
+		}
+
+		codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		return codeSystem;
+
+	}
+
+	private void testCreatingAndUpdatingCodeSystemEntity(CodeSystem theUpload, CodeSystem theDuplicate, int expectedCnt, String theDuplicateErrorBaseMsg) {
+
+		// Create CodeSystem resource
+		ResourceTable codeSystemResourceEntity = (ResourceTable) myCodeSystemDao.create(theUpload, mySrd).getEntity();
+
+		// Create the CodeSystem and CodeSystemVersion entities
+		validateCodeSystemUpdates(expectedCnt);
+
+		// Update the CodeSystem
+		theUpload.addConcept(new CodeSystem.ConceptDefinitionComponent(new CodeType("codeB")));
+		// Update the CodeSystem and CodeSystemVersion entities
+		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(theUpload, codeSystemResourceEntity));
+		validateCodeSystemUpdates(expectedCnt+1);
+
+		// Try duplicating the CodeSystem
+		Long originalResId = codeSystemResourceEntity.getId();
+		try {
+			myCodeSystemDao.create(theDuplicate, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals(theDuplicateErrorBaseMsg + originalResId, e.getMessage());
+		}
+
+		// Try updating code system when content mode is NOT PRESENT
+		theUpload.setConcept(new ArrayList<>());
+		theUpload.setContent((CodeSystem.CodeSystemContentMode.NOTPRESENT));
+		runInTransaction(() -> myTermCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(theUpload, codeSystemResourceEntity));
+		validateCodeSystemUpdates(expectedCnt+1);
+
+	}
+
+	private void validateCodeSystemUpdates(int theExpectedConceptCount) {
+		myTerminologyDeferredStorageSvc.setProcessDeferred(true);
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myTerminologyDeferredStorageSvc.setProcessDeferred(false);
+		assertEquals(theExpectedConceptCount, myTermConceptDao.count());
+
+	}
 
 }

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

@@ -351,12 +351,21 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		CodeSystem loincCS = mySystemCaptor.getValue();
 		assertEquals("2.67", loincCS.getVersion());
 
+		// Update LOINC marked as version 2.67
+		myFiles = new ZipCollectionBuilder();
+		addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+
+		verify(myTermCodeSystemStorageSvc, times(2)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		loincCS = mySystemCaptor.getValue();
+		assertEquals("2.67", loincCS.getVersion());
+
 		// Load LOINC marked as version 2.68
 		myFiles = new ZipCollectionBuilder();
 		addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v268_loincupload.properties");
 		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 
-		verify(myTermCodeSystemStorageSvc, times(2)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		verify(myTermCodeSystemStorageSvc, times(3)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		loincCS = mySystemCaptor.getValue();
 		assertEquals("2.68", loincCS.getVersion());
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java

@@ -12,7 +12,6 @@ import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
 import ca.uhn.fhir.jpa.entity.TermValueSet;
-import ca.uhn.fhir.model.dstu2.valueset.ContentTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CanonicalType;
@@ -25,7 +24,6 @@ import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
 import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.HttpVerb;
-import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -1787,10 +1785,10 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
 		createCodeSystem();
 
 		IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(new ValidationSupportContext(myValidationSupport), new ConceptValidationOptions(), CS_URL, "ParentWithNoChildrenA", null, null);
-		assertEquals(true, validation.isOk());
+		assertTrue(validation.isOk());
 
 		validation = myTermSvc.validateCode(new ValidationSupportContext(myValidationSupport), new ConceptValidationOptions(), CS_URL, "ZZZZZZZ", null, null);
-		assertEquals(false, validation.isOk());
+		assertFalse(validation.isOk());
 	}
 
 	@Test
@@ -1927,8 +1925,8 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
 		codeSystem
 			.addConcept().setCode("C").setDisplay("Code C");
 
-		myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+		IIdType id_v2 = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
-		codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "C");
+		codes = myTermSvc.findCodesBelow(id_v2.getIdPartAsLong(), id_v2.getVersionIdPartAsLong(), "C");
 		assertThat(toCodes(codes), containsInAnyOrder("C"));
 
 		runInTransaction(() -> {
@@ -1939,7 +1937,7 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
 			Set<TermConcept> termConcepts_updated = new HashSet<>(termCodeSystemVersion_2.getConcepts());
 			assertThat(toCodes(termConcepts_updated), containsInAnyOrder("A", "B", "C"));
 
-			TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id.getIdPartAsLong());
+			TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id_v2.getIdPartAsLong());
 			assertEquals("2", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
 		});
 	}