loinc updates

example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/CdsServerExample.java

@@ -5,9 +5,9 @@
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
+import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.rp.dstu3.ActivityDefinitionResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu3.MeasureResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu3.PlanDefinitionResourceProvider;
@@ -149,7 +149,7 @@ protected void initialize() throws ServletException {
 		 * so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
 		 * with this feature.
 		 */
-		registerProvider(myAppCtx.getBean(TerminologyUploaderProvider.class));
+		registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
 	}
 
 	public IResourceProvider getProvider(String name) {

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -8,9 +8,10 @@
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
+import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
 import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
@@ -78,10 +79,10 @@ protected void initialize() throws ServletException {
 			systemProvider.add(myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class));
 		} else if (fhirVersion == FhirVersionEnum.DSTU3) {
 			systemProvider.add(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
-			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
+			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
 		} else if (fhirVersion == FhirVersionEnum.R4) {
 			systemProvider.add(myAppCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class));
-			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
+			systemProvider.add(myAppCtx.getBean(TerminologyUploaderProviderR4.class));
 		} else {
 			throw new IllegalStateException();
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -9,8 +9,11 @@
 import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.dao.dstu3.SearchParamExtractorDstu3;
 import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
-import ca.uhn.fhir.jpa.term.*;
+import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
+import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu3;
+import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
+import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
@@ -115,8 +118,8 @@ public IHapiTerminologySvcDstu3 terminologyService() {
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public TerminologyUploaderProvider terminologyUploaderProvider() {
-		TerminologyUploaderProvider retVal = new TerminologyUploaderProvider();
+	public TerminologyUploaderProviderDstu3 terminologyUploaderProvider() {
+		TerminologyUploaderProviderDstu3 retVal = new TerminologyUploaderProviderDstu3();
 		retVal.setContext(fhirContextDstu3());
 		return retVal;
 	}
@@ -126,5 +129,5 @@ public TerminologyUploaderProvider terminologyUploaderProvider() {
 	public IValidationSupport validationSupportChainDstu3() {
 		return new JpaValidationSupportChainDstu3();
 	}
-	
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java

@@ -10,7 +10,7 @@
 import ca.uhn.fhir.jpa.dao.r4.SearchParamExtractorR4;
 import ca.uhn.fhir.jpa.dao.r4.SearchParamRegistryR4;
 import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
 import ca.uhn.fhir.jpa.term.HapiTerminologySvcR4;
 import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
@@ -133,8 +133,8 @@ public IHapiTerminologySvcR4 terminologyService() {
 	}
 
 	@Bean(autowire = Autowire.BY_TYPE)
-	public TerminologyUploaderProvider terminologyUploaderProvider() {
-		TerminologyUploaderProvider retVal = new TerminologyUploaderProvider();
+	public TerminologyUploaderProviderR4 terminologyUploaderProvider() {
+		TerminologyUploaderProviderR4 retVal = new TerminologyUploaderProviderR4();
 		retVal.setContext(fhirContextR4());
 		return retVal;
 	}

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

@@ -44,10 +44,12 @@
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.server.exceptions.*;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
+import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.*;
 import com.google.common.annotations.VisibleForTesting;
@@ -67,7 +69,6 @@
 import org.hl7.fhir.r4.model.BaseResource;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Reference;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
@@ -110,6 +111,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	private static final Map<FhirVersionEnum, FhirContext> ourRetrievalContexts = new HashMap<FhirVersionEnum, FhirContext>();
 	private static final String PROCESSING_SUB_REQUEST = "BaseHapiFhirDao.processingSubRequest";
 	private static boolean ourValidationDisabledForUnitTest;
+	private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
 
 	static {
 		Map<String, Class<? extends IQueryParameterType>> resourceMetaParams = new HashMap<String, Class<? extends IQueryParameterType>>();
@@ -834,6 +836,22 @@ protected IBundleProvider history(String theResourceName, Long theId, Date theSi
 		return new PersistedJpaBundleProvider(search.getUuid(), this);
 	}
 
+	void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
+		String newVersion;
+		long newVersionLong;
+		if (theResourceId == null || theResourceId.getVersionIdPart() == null) {
+			newVersion = "1";
+			newVersionLong = 1;
+		} else {
+			newVersionLong = theResourceId.getVersionIdPartAsLong() + 1;
+			newVersion = Long.toString(newVersionLong);
+		}
+
+		IIdType newId = theResourceId.withVersion(newVersion);
+		theResource.getIdElement().setValue(newId.getValue());
+		theSavedEntity.setVersion(newVersionLong);
+	}
+
 	@Override
 	public void injectDependenciesIntoBundleProvider(PersistedJpaBundleProvider theProvider) {
 		theProvider.setContext(getContext());
@@ -1816,6 +1834,55 @@ protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable en
 		return updateEntity(theResource, entity, theDeletedTimestampOrNull, true, true, theUpdateTime, false, true);
 	}
 
+	public ResourceTable updateInternal(T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion, RequestDetails theRequestDetails, ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource) {
+		// Notify interceptors
+		ActionRequestDetails requestDetails = null;
+		if (theRequestDetails != null) {
+			requestDetails = new ActionRequestDetails(theRequestDetails, theResource, theResourceId.getResourceType(), theResourceId);
+			notifyInterceptors(RestOperationTypeEnum.UPDATE, requestDetails);
+		}
+
+		// Notify IServerOperationInterceptors about pre-action call
+		if (theRequestDetails != null) {
+			theRequestDetails.getRequestOperationCallback().resourcePreUpdate(theOldResource, theResource);
+		}
+		for (IServerInterceptor next : getConfig().getInterceptors()) {
+			if (next instanceof IServerOperationInterceptor) {
+				((IServerOperationInterceptor) next).resourcePreUpdate(theRequestDetails, theOldResource, theResource);
+			}
+		}
+
+		// Perform update
+		ResourceTable savedEntity = updateEntity(theResource, theEntity, null, thePerformIndexing, thePerformIndexing, new Date(), theForceUpdateVersion, thePerformIndexing);
+
+		/*
+		 * If we aren't indexing (meaning we're probably executing a sub-operation within a transaction),
+		 * we'll manually increase the version. This is important because we want the updated version number
+		 * to be reflected in the resource shared with interceptors
+		 */
+		if (!thePerformIndexing && !savedEntity.isUnchangedInCurrentOperation() && !ourDisableIncrementOnUpdateForUnitTest) {
+			if (theResourceId.hasVersionIdPart() == false) {
+				theResourceId = theResourceId.withVersion(Long.toString(savedEntity.getVersion()));
+			}
+			incrementId(theResource, savedEntity, theResourceId);
+		}
+
+		// Notify interceptors
+		if (!savedEntity.isUnchangedInCurrentOperation()) {
+			if (theRequestDetails != null) {
+				theRequestDetails.getRequestOperationCallback().resourceUpdated(theResource);
+				theRequestDetails.getRequestOperationCallback().resourceUpdated(theOldResource, theResource);
+			}
+			for (IServerInterceptor next : getConfig().getInterceptors()) {
+				if (next instanceof IServerOperationInterceptor) {
+					((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, theResource);
+					((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, theOldResource, theResource);
+				}
+			}
+		}
+		return savedEntity;
+	}
+
 	private void validateChildReferences(IBase theElement, String thePath) {
 		if (theElement == null) {
 			return;
@@ -2133,6 +2200,11 @@ private static String parseNarrativeTextIntoWords(IBaseResource theResource) {
 		return b.toString();
 	}
 
+	@VisibleForTesting
+	public static void setDisableIncrementOnUpdateForUnitTest(boolean theDisableIncrementOnUpdateForUnitTest) {
+		ourDisableIncrementOnUpdateForUnitTest = theDisableIncrementOnUpdateForUnitTest;
+	}
+
 	/**
 	 * Do not call this method outside of unit tests
 	 */

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

@@ -77,7 +77,6 @@
 public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
-	private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired
@@ -592,22 +591,6 @@ public IBundleProvider history(final IIdType theId, final Date theSince, Date th
 		return retVal;
 	}
 
-	private void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
-		String newVersion;
-		long newVersionLong;
-		if (theResourceId == null || theResourceId.getVersionIdPart() == null) {
-			newVersion = "1";
-			newVersionLong = 1;
-		} else {
-			newVersionLong = theResourceId.getVersionIdPartAsLong() + 1;
-			newVersion = Long.toString(newVersionLong);
-		}
-
-		IIdType newId = theResourceId.withVersion(newVersion);
-		theResource.getIdElement().setValue(newId.getValue());
-		theSavedEntity.setVersion(newVersionLong);
-	}
-
 	protected boolean isPagingProviderDatabaseBacked(RequestDetails theRequestDetails) {
 		if (theRequestDetails == null || theRequestDetails.getServer() == null) {
 			return false;
@@ -1229,54 +1212,24 @@ public DaoMethodOutcome update(T theResource, String theMatchUrl, boolean thePer
 				"Invalid resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] of type[" + entity.getResourceType() + "] - Does not match expected [" + getResourceName() + "]");
 		}
 
-		// Notify interceptors
-		ActionRequestDetails requestDetails = null;
-		if (theRequestDetails != null) {
-			requestDetails = new ActionRequestDetails(theRequestDetails, theResource, getResourceName(), resourceId);
-			notifyInterceptors(RestOperationTypeEnum.UPDATE, requestDetails);
-		}
-
 		IBaseResource oldResource = toResource(entity, false);
 
-		// Notify IServerOperationInterceptors about pre-action call
-		if (theRequestDetails != null) {
-			theRequestDetails.getRequestOperationCallback().resourcePreUpdate(oldResource, theResource);
-		}
-		for (IServerInterceptor next : getConfig().getInterceptors()) {
-			if (next instanceof IServerOperationInterceptor) {
-				((IServerOperationInterceptor) next).resourcePreUpdate(theRequestDetails, oldResource, theResource);
-			}
-		}
-
-		// Perform update
-		ResourceTable savedEntity = updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, new Date(), theForceUpdateVersion, thePerformIndexing);
-
 		/*
-		 * If we aren't indexing (meaning we're probably executing a sub-operation within a transaction),
-		 * we'll manually increase the version. This is important because we want the updated version number
-		 * to be reflected in the resource shared with interceptors
+		 * If we aren't indexing, that means we're doing this inside a transaction.
+		 * The transaction will do the actual storate to the database a bit later on,
+		 * after placeholder IDs have been replaced, by calling {@link #updateInternal}
+		 * directly. So we just bail now.
 		 */
-		if (!thePerformIndexing && !savedEntity.isUnchangedInCurrentOperation() && !ourDisableIncrementOnUpdateForUnitTest) {
-			if (resourceId.hasVersionIdPart() == false) {
-				resourceId = resourceId.withVersion(Long.toString(savedEntity.getVersion()));
-			}
-			incrementId(theResource, savedEntity, resourceId);
-		}
-
-		// Notify interceptors
-		if (!savedEntity.isUnchangedInCurrentOperation()) {
-			if (theRequestDetails != null) {
-				theRequestDetails.getRequestOperationCallback().resourceUpdated(theResource);
-				theRequestDetails.getRequestOperationCallback().resourceUpdated(oldResource, theResource);
-			}
-			for (IServerInterceptor next : getConfig().getInterceptors()) {
-				if (next instanceof IServerOperationInterceptor) {
-					((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, theResource);
-					((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, oldResource, theResource);
-				}
-			}
+		if (!thePerformIndexing) {
+			DaoMethodOutcome outcome = toMethodOutcome(entity, theResource).setCreated(false);
+			outcome.setPreviousResource(oldResource);
+			return outcome;
 		}
 
+		/*
+		 * Otherwise, we're not in a transaction
+		 */
+		ResourceTable savedEntity = updateInternal(theResource, thePerformIndexing, theForceUpdateVersion, theRequestDetails, entity, resourceId, oldResource);
 		DaoMethodOutcome outcome = toMethodOutcome(savedEntity, theResource).setCreated(false);
 
 		if (!thePerformIndexing) {
@@ -1366,9 +1319,5 @@ private void validateResourceTypeAndThrowIllegalArgumentException(IIdType theId)
 		}
 	}
 
-	@VisibleForTesting
-	public static void setDisableIncrementOnUpdateForUnitTest(boolean theDisableIncrementOnUpdateForUnitTest) {
-		ourDisableIncrementOnUpdateForUnitTest = theDisableIncrementOnUpdateForUnitTest;
-	}
 
 }

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

@@ -22,24 +22,41 @@
 
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.rest.api.MethodOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
 public class DaoMethodOutcome extends MethodOutcome {
 
 	private ResourceTable myEntity;
+	private IBaseResource myPreviousResource;
 
 	public ResourceTable getEntity() {
 		return myEntity;
 	}
 
-	@Override
-	public DaoMethodOutcome setCreated(Boolean theCreated) {
-		super.setCreated(theCreated);
-		return this;
-	}
-
 	public DaoMethodOutcome setEntity(ResourceTable theEntity) {
 		myEntity = theEntity;
 		return this;
 	}
 
+	/**
+	 * For update operations, this is the body of the resource as it was before the
+	 * update
+	 */
+	public IBaseResource getPreviousResource() {
+		return myPreviousResource;
+	}
+
+	/**
+	 * For update operations, this is the body of the resource as it was before the
+	 * update
+	 */
+	public void setPreviousResource(IBaseResource thePreviousResource) {
+		myPreviousResource = thePreviousResource;
+	}
+
+	@Override
+	public DaoMethodOutcome setCreated(Boolean theCreated) {
+		super.setCreated(theCreated);
+		return this;
+	}
 }