Resolve "Need to implement the ancestor and descendant filters for LOINC."

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

@@ -9,7 +9,6 @@
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
 import ca.uhn.fhir.jpa.provider.GraphQLProvider;
-import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu3;
@@ -21,6 +20,7 @@
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.dstu3.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
@@ -99,6 +99,11 @@ public IValidatorModule instanceValidatorDstu3() {
 		return val;
 	}
 
+	@Bean
+	public DefaultProfileValidationSupport defaultProfileValidationSupport() {
+		return new DefaultProfileValidationSupport();
+	}
+
 	@Bean
 	public JpaValidationSupportChainDstu3 jpaValidationSupportChain() {
 		return new JpaValidationSupportChainDstu3();

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

@@ -8,7 +8,7 @@
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
-import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
@@ -20,14 +20,12 @@
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import org.hl7.fhir.r4.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.utils.GraphQLEngine;
 import org.hl7.fhir.r5.utils.IResourceValidator;
-import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -102,6 +100,11 @@ public IValidatorModule instanceValidatorR4() {
 		return val;
 	}
 
+	@Bean
+	public DefaultProfileValidationSupport defaultProfileValidationSupport() {
+		return new DefaultProfileValidationSupport();
+	}
+
 	@Bean
 	public JpaValidationSupportChainR4 jpaValidationSupportChain() {
 		return new JpaValidationSupportChainR4();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java

@@ -20,6 +20,7 @@
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR5;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r5.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.r5.hapi.validation.FhirInstanceValidator;
@@ -99,6 +100,11 @@ public IValidatorModule instanceValidatorR5() {
 		return val;
 	}
 
+	@Bean
+	public DefaultProfileValidationSupport defaultProfileValidationSupport() {
+		return new DefaultProfileValidationSupport();
+	}
+
 	@Bean
 	public JpaValidationSupportChainR5 jpaValidationSupportChain() {
 		return new JpaValidationSupportChainR5();

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

@@ -112,7 +112,7 @@
 
 @SuppressWarnings("WeakerAccess")
 @Repository
-public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao, ApplicationContextAware {
+public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao, IJpaDao<T>, ApplicationContextAware {
 
 	public static final long INDEX_STATUS_INDEXED = 1L;
 	public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
@@ -1017,7 +1017,8 @@ protected ResourceTable updateEntityForDelete(RequestDetails theRequest, Resourc
 	}
 
 	@SuppressWarnings("unchecked")
-	protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
+	@Override
+	public ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
 		theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		Validate.notNull(theEntity);
@@ -1256,6 +1257,7 @@ protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResou
 		return theEntity;
 	}
 
+	@Override
 	public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
 													ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource) {
 

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

@@ -149,21 +149,29 @@ public class DaoConfig {
 	private boolean myFilterParameterEnabled = false;
 	private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
 	/**
-	 * EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
+	 * Do not change default of {@code true}!
+	 *
+	 * @since 4.1.0
 	 */
-	private boolean myPreExpandValueSetsExperimental = false;
+	private boolean myPreExpandValueSets = true;
 	/**
-	 * EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
+	 * Do not change default of {@code 0}!
+	 *
+	 * @since 4.1.0
 	 */
-	private int myPreExpandValueSetsDefaultOffsetExperimental = 0;
+	private int myPreExpandValueSetsDefaultOffset = 0;
 	/**
-	 * EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
+	 * Do not change default of {@code 1000}!
+	 *
+	 * @since 4.1.0
 	 */
-	private int myPreExpandValueSetsDefaultCountExperimental = 1000;
+	private int myPreExpandValueSetsDefaultCount = 1000;
 	/**
-	 * EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
+	 * Do not change default of {@code 1000}!
+	 *
+	 * @since 4.1.0
 	 */
-	private int myPreExpandValueSetsMaxCountExperimental = 1000;
+	private int myPreExpandValueSetsMaxCount = 1000;
 
 	/**
 	 * Constructor
@@ -920,7 +928,7 @@ public boolean isAllowInlineMatchUrlReferences() {
 	 * <p>
 	 * Default is {@literal true} beginning in HAPI FHIR 2.4, since this
 	 * feature is now specified in the FHIR specification. (Previously it
-	 * was an experimental/rpposed feature)
+	 * was an experimental/proposed feature)
 	 * </p>
 	 *
 	 * @since 1.5
@@ -1621,34 +1629,6 @@ public void setWebsocketContextPath(String theWebsocketContextPath) {
 		myModelConfig.setWebsocketContextPath(theWebsocketContextPath);
 	}
 
-	/**
-	 * EXPERIMENTAL - Do not use in production!
-	 * <p>
-	 * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
-	 * future optimization of the $expand operation on large ValueSets.
-	 * </p>
-	 * <p>
-	 * The default value for this setting is {@code false}.
-	 * </p>
-	 */
-	public boolean isPreExpandValueSetsExperimental() {
-		return myPreExpandValueSetsExperimental;
-	}
-
-	/**
-	 * EXPERIMENTAL - Do not use in production!
-	 * <p>
-	 * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
-	 * future optimization of the $expand operation on large ValueSets.
-	 * </p>
-	 * <p>
-	 * The default value for this setting is {@code false}.
-	 * </p>
-	 */
-	public void setPreExpandValueSetsExperimental(boolean thePreExpandValueSetsExperimental) {
-		myPreExpandValueSetsExperimental = thePreExpandValueSetsExperimental;
-	}
-
 	/**
 	 * If set to <code>true</code> the _filter search parameter will be enabled on this server. Note that _filter
 	 * is very powerful, but also potentially dangerous as it can allow a user to create a query for which there
@@ -1720,83 +1700,118 @@ public boolean isStoreRequestId() {
 	}
 
 	/**
-	 * EXPERIMENTAL - Do not use in production!
+	 * <p>
+	 * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
+	 * optimization of the $expand operation on large ValueSets.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code true}.
+	 * </p>
+	 *
+	 * @since 4.1.0
+	 */
+	public boolean isPreExpandValueSets() {
+		return myPreExpandValueSets;
+	}
+
+	/**
+	 * <p>
+	 * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
+	 * optimization of the $expand operation on large ValueSets.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code true}.
+	 * </p>
+	 *
+	 * @since 4.1.0
+	 */
+	public void setPreExpandValueSets(boolean thePreExpandValueSets) {
+		myPreExpandValueSets = thePreExpandValueSets;
+	}
+
+	/**
 	 * <p>
 	 * This is the default value of {@code offset} parameter for the ValueSet {@code $expand} operation when
-	 * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+	 * {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
 	 * </p>
 	 * <p>
 	 * The default value for this setting is {@code 0}.
 	 * </p>
+	 *
+	 * @since 4.1.0
 	 */
-	public int getPreExpandValueSetsDefaultOffsetExperimental() {
-		return myPreExpandValueSetsDefaultOffsetExperimental;
+	public int getPreExpandValueSetsDefaultOffset() {
+		return myPreExpandValueSetsDefaultOffset;
 	}
 
 	/**
-	 * EXPERIMENTAL - Do not use in production!
 	 * <p>
 	 * This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
-	 * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+	 * {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
 	 * </p>
 	 * <p>
 	 * The default value for this setting is {@code 1000}.
 	 * </p>
+	 *
+	 * @since 4.1.0
 	 */
-	public int getPreExpandValueSetsDefaultCountExperimental() {
-		return myPreExpandValueSetsDefaultCountExperimental;
+	public int getPreExpandValueSetsDefaultCount() {
+		return myPreExpandValueSetsDefaultCount;
 	}
 
 	/**
-	 * EXPERIMENTAL - Do not use in production!
 	 * <p>
 	 * This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
-	 * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+	 * {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
 	 * </p>
 	 * <p>
-	 * If {@code thePreExpandValueSetsDefaultCountExperimental} is greater than
-	 * {@link DaoConfig#getPreExpandValueSetsMaxCountExperimental()}, the lesser value is used.
+	 * If {@code thePreExpandValueSetsDefaultCount} is greater than
+	 * {@link DaoConfig#getPreExpandValueSetsMaxCount()}, the lesser value is used.
 	 * </p>
 	 * <p>
 	 * The default value for this setting is {@code 1000}.
 	 * </p>
+	 *
+	 * @since 4.1.0
 	 */
-	public void setPreExpandValueSetsDefaultCountExperimental(int thePreExpandValueSetsDefaultCountExperimental) {
-		myPreExpandValueSetsDefaultCountExperimental = Math.min(thePreExpandValueSetsDefaultCountExperimental, getPreExpandValueSetsMaxCountExperimental());
+	public void setPreExpandValueSetsDefaultCount(int thePreExpandValueSetsDefaultCount) {
+		myPreExpandValueSetsDefaultCount = Math.min(thePreExpandValueSetsDefaultCount, getPreExpandValueSetsMaxCount());
 	}
 
 	/**
-	 * EXPERIMENTAL - Do not use in production!
 	 * <p>
 	 * This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
-	 * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+	 * {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
 	 * </p>
 	 * <p>
 	 * The default value for this setting is {@code 1000}.
 	 * </p>
+	 *
+	 * @since 4.1.0
 	 */
-	public int getPreExpandValueSetsMaxCountExperimental() {
-		return myPreExpandValueSetsMaxCountExperimental;
+	public int getPreExpandValueSetsMaxCount() {
+		return myPreExpandValueSetsMaxCount;
 	}
 
 	/**
-	 * EXPERIMENTAL - Do not use in production!
 	 * <p>
 	 * This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
-	 * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+	 * {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
 	 * </p>
 	 * <p>
-	 * If {@code thePreExpandValueSetsMaxCountExperimental} is lesser than
-	 * {@link DaoConfig#getPreExpandValueSetsDefaultCountExperimental()}, the default {@code count} is lowered to the
+	 * If {@code thePreExpandValueSetsMaxCount} is lesser than
+	 * {@link DaoConfig#getPreExpandValueSetsDefaultCount()}, the default {@code count} is lowered to the
 	 * new max {@code count}.
 	 * </p>
 	 * <p>
 	 * The default value for this setting is {@code 1000}.
 	 * </p>
+	 *
+	 * @since 4.1.0
 	 */
-	public void setPreExpandValueSetsMaxCountExperimental(int thePreExpandValueSetsMaxCountExperimental) {
-		myPreExpandValueSetsMaxCountExperimental = thePreExpandValueSetsMaxCountExperimental;
-		setPreExpandValueSetsDefaultCountExperimental(Math.min(getPreExpandValueSetsDefaultCountExperimental(), getPreExpandValueSetsMaxCountExperimental()));
+	public void setPreExpandValueSetsMaxCount(int thePreExpandValueSetsMaxCount) {
+		myPreExpandValueSetsMaxCount = thePreExpandValueSetsMaxCount;
+		setPreExpandValueSetsDefaultCount(Math.min(getPreExpandValueSetsDefaultCount(), getPreExpandValueSetsMaxCount()));
 	}
 
 	public enum IndexEnabledEnum {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java

@@ -73,8 +73,8 @@ protected void postPersist(ResourceTable theEntity, Subscription theSubscription
 
 
 	@Override
-	protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
-													 Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
+												 Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
 		if (theDeletedTimestampOrNull != null) {

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

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.jpa.dao;
+
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import java.util.Date;
+
+public interface IJpaDao<T extends IBaseResource> {
+	@SuppressWarnings("unchecked")
+	ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable
+		theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+										boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry);
+
+	ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
+										  ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource);
+}

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

@@ -909,10 +909,13 @@ private Map<BUNDLEENTRY, ResourceTable> doTransactionWriteOperations(final Servl
 				IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
 				Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
 
+				IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(nextResource.getClass());
+				IJpaDao jpaDao = (IJpaDao) dao;
+
 				if (updatedEntities.contains(nextOutcome.getEntity())) {
-					myDao.updateInternal(theRequest, nextResource, true, false, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
+					jpaDao.updateInternal(theRequest, nextResource, true, false, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
 				} else if (!nonUpdatedEntities.contains(nextOutcome.getEntity())) {
-					myDao.updateEntity(theRequest, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
+					jpaDao.updateEntity(theRequest, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
 				}
 			}
 

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

@@ -125,8 +125,8 @@ protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntity
 	}
 
 	@Override
-	protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
-													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
 		CodeSystem csDstu3 = (CodeSystem) theResource;