Merge remote-tracking branch 'remotes/origin/master' into ks-flyway

examples/src/main/java/example/ValidateSimple.java

@@ -0,0 +1,43 @@
+package example;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ValidationResult;
+import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+
+import java.io.FileReader;
+
+public class ValidateSimple {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidateSimple.class);
+
+	public static void main(String[] args) throws Exception {
+		FhirContext ctx = FhirContext.forR4();
+
+		// Create a validator module
+		FhirInstanceValidator instanceValidator = new FhirInstanceValidator();
+
+		// We'll create a validation chain with only the DefaultProfileValidationupport registered
+		ValidationSupportChain validationSupportChain = new ValidationSupportChain();
+		validationSupportChain.addValidationSupport(new DefaultProfileValidationSupport());
+		instanceValidator.setValidationSupport(validationSupportChain);
+
+		// Create a validator and register the InstanceValidator module
+		FhirValidator val = ctx.newValidator();
+		val.registerValidatorModule(instanceValidator);
+
+		// Read in the file and validate it
+		String nextFile = args[0];
+		try (FileReader fileReader = new FileReader(nextFile)) {
+			String input = IOUtils.toString(fileReader);
+			ValidationResult result = val.validateWithResult(input);
+			IBaseOperationOutcome oo = result.toOperationOutcome();
+			ourLog.info("Result:\n{}", ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
+		}
+
+	}
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java

@@ -1,19 +1,27 @@
 package ca.uhn.fhir.context;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
-import static org.apache.commons.lang3.StringUtils.trim;
-
-import java.util.*;
-
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
-
 import javax.annotation.Nonnull;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.StringTokenizer;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 /*
  * #%L
@@ -44,61 +52,22 @@ public class RuntimeSearchParam {
 	private final RestSearchParameterTypeEnum myParamType;
 	private final String myPath;
 	private final Set<String> myTargets;
-
-	@Override
-	public String toString() {
-		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
-			.append("base", myBase)
-			.append("name", myName)
-			.append("path", myPath)
-			.append("id", myId)
-			.append("uri", myUri)
-			.toString();
-	}
-
 	private final Set<String> myProvidesMembershipInCompartments;
 	private final RuntimeSearchParamStatusEnum myStatus;
 	private final String myUri;
+	private final Map<String, List<IBaseExtension<?, ?>>> myExtensions = new HashMap<>();
 
-	public IIdType getId() {
+	/**
-		return myId;
+	 * Constructor
-	}
+	 */
-
-	public String getUri() {
-		return myUri;
-	}
-
 	public RuntimeSearchParam(IIdType theId, String theUri, String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf,
 									  Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus) {
 		this(theId, theUri, theName, theDescription, thePath, theParamType, theCompositeOf, theProvidesMembershipInCompartments, theTargets, theStatus, null);
 	}
 
-	@Override
+	/**
-	public boolean equals(Object theO) {
+	 * Constructor
-		if (this == theO) return true;
+	 */
-
-		if (theO == null || getClass() != theO.getClass()) return false;
-
-		RuntimeSearchParam that = (RuntimeSearchParam) theO;
-
-		return new EqualsBuilder()
-			.append(getId(), that.getId())
-			.append(getName(), that.getName())
-			.append(getPath(), that.getPath())
-			.append(getUri(), that.getUri())
-			.isEquals();
-	}
-
-	@Override
-	public int hashCode() {
-		return new HashCodeBuilder(17, 37)
-			.append(getId())
-			.append(getName())
-			.append(getPath())
-			.append(getUri())
-			.toHashCode();
-	}
-
 	public RuntimeSearchParam(IIdType theId, String theUri, String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf,
 									  Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus, Collection<String> theBase) {
 		super();
@@ -136,6 +105,77 @@ public class RuntimeSearchParam {
 		}
 	}
 
+	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus) {
+		this(null, null, theName, theDescription, thePath, theParamType, null, theProvidesMembershipInCompartments, theTargets, theStatus);
+	}
+
+	/**
+	 * Retrieve user data - This can be used to store any application-specific data
+	 *
+	 * @return
+	 */
+	public List<IBaseExtension<?, ?>> getExtensions(String theKey) {
+		List<IBaseExtension<?, ?>> retVal = myExtensions.get(theKey);
+		if (retVal != null) {
+			retVal = Collections.unmodifiableList(retVal);
+		}
+		return retVal;
+	}
+
+	/**
+	 * Sets user data - This can be used to store any application-specific data
+	 */
+	public RuntimeSearchParam addExtension(String theKey, IBaseExtension theValue) {
+		List<IBaseExtension<?, ?>> valuesList = myExtensions.computeIfAbsent(theKey, k -> new ArrayList<>());
+		valuesList.add(theValue);
+		return this;
+	}
+
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
+			.append("base", myBase)
+			.append("name", myName)
+			.append("path", myPath)
+			.append("id", myId)
+			.append("uri", myUri)
+			.toString();
+	}
+
+	public IIdType getId() {
+		return myId;
+	}
+
+	public String getUri() {
+		return myUri;
+	}
+
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) return true;
+
+		if (theO == null || getClass() != theO.getClass()) return false;
+
+		RuntimeSearchParam that = (RuntimeSearchParam) theO;
+
+		return new EqualsBuilder()
+			.append(getId(), that.getId())
+			.append(getName(), that.getName())
+			.append(getPath(), that.getPath())
+			.append(getUri(), that.getUri())
+			.isEquals();
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(17, 37)
+			.append(getId())
+			.append(getName())
+			.append(getPath())
+			.append(getUri())
+			.toHashCode();
+	}
+
 	public Set<String> getBase() {
 		return myBase;
 	}
@@ -153,10 +193,6 @@ public class RuntimeSearchParam {
 		return myStatus;
 	}
 
-	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus) {
-		this(null, null, theName, theDescription, thePath, theParamType, null, theProvidesMembershipInCompartments, theTargets, theStatus);
-	}
-
 	public List<RuntimeSearchParam> getCompositeOf() {
 		return myCompositeOf;
 	}
@@ -206,5 +242,5 @@ public class RuntimeSearchParam {
 		RETIRED,
 		UNKNOWN
 	}
-	
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ReflectionUtil.java

@@ -118,11 +118,10 @@ public class ReflectionUtil {
 	/**
 	 * Instantiate a class by no-arg constructor, throw {@link ConfigurationException} if we fail to do so
 	 */
-	@CoverageIgnore
 	public static <T> T newInstance(Class<T> theType) {
 		Validate.notNull(theType, "theType must not be null");
 		try {
-			return theType.newInstance();
+			return theType.getConstructor().newInstance();
 		} catch (Exception e) {
 			throw new ConfigurationException("Failed to instantiate " + theType.getName(), e);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImpl.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IResultIterator;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
@@ -251,7 +252,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 			OutputStreamWriter writer = new OutputStreamWriter(outputStream, Constants.CHARSET_UTF8);
 			IParser parser = myContext.newJsonParser().setPrettyPrint(false);
 
-			List<Long> pidsSpool = new ArrayList<>();
+			List<ResourcePersistentId> pidsSpool = new ArrayList<>();
 			List<IBaseResource> resourcesSpool = new ArrayList<>();
 			while (query.hasNext()) {
 				pidsSpool.add(query.next());

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

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.bulk.BulkDataExportSvcImpl;
 import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.delete.DeleteConflictService;
 import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
 import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
 import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
@@ -26,6 +27,8 @@ import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
 import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.subscription.SubscriptionActivatingInterceptor;
 import ca.uhn.fhir.jpa.subscription.dbmatcher.CompositeInMemoryDaoSubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.dbmatcher.DaoSubscriptionMatcher;
@@ -129,6 +132,12 @@ public abstract class BaseConfig {
 		return b;
 	}
 
+	@Bean
+	public ISearchParamRegistry searchParamRegistry() {
+		return new SearchParamRegistryImpl();
+	}
+
+
 	@Bean(name = "mySubscriptionTriggeringProvider")
 	@Lazy
 	public SubscriptionTriggeringProvider subscriptionTriggeringProvider() {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java

@@ -5,16 +5,11 @@ import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu2;
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu2;
 import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
-import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
-import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu2;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
-import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
@@ -117,11 +112,6 @@ public class BaseDstu2Config extends BaseConfig {
 		return new SearchParamExtractorDstu2();
 	}
 
-	@Bean
-	public ISearchParamRegistry searchParamRegistry() {
-		return new SearchParamRegistryDstu2();
-	}
-
 	@Bean(name = "mySystemDaoDstu2", autowire = Autowire.BY_NAME)
 	public IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDaoDstu2() {
 		ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2 retVal = new ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2();

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

@@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.config.dstu3;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
-import ca.uhn.fhir.jpa.config.BaseConfig;
 import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
@@ -11,24 +10,20 @@ 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.searchparam.extractor.SearchParamExtractorDstu3;
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu3;
-import ca.uhn.fhir.jpa.term.TermReadSvcDstu3;
 import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
+import ca.uhn.fhir.jpa.term.TermReadSvcDstu3;
 import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu3;
-import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
-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;
-import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -95,8 +90,8 @@ public class BaseDstu3Config extends BaseConfigDstu3Plus {
 	}
 
 	@Bean
-	public TransactionProcessor<Bundle, Bundle.BundleEntryComponent> transactionProcessor() {
+	public TransactionProcessor transactionProcessor() {
-		return new TransactionProcessor<>();
+		return new TransactionProcessor();
 	}
 
 	@Bean(name = "myInstanceValidatorDstu3")
@@ -140,11 +135,6 @@ public class BaseDstu3Config extends BaseConfigDstu3Plus {
 		return new SearchParamExtractorDstu3();
 	}
 
-	@Bean
-	public ISearchParamRegistry searchParamRegistry() {
-		return new SearchParamRegistryDstu3();
-	}
-
 	@Bean(name = "mySystemDaoDstu3")
 	public IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDaoDstu3() {
 		return new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();

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

@@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.config.r4;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
-import ca.uhn.fhir.jpa.config.BaseConfig;
 import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
@@ -11,22 +10,20 @@ import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
 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.term.TermLoaderSvcImpl;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
+import ca.uhn.fhir.jpa.term.TermReadSvcR4;
-import ca.uhn.fhir.jpa.term.*;
+import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcR4;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
-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 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.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
@@ -88,8 +85,8 @@ public class BaseR4Config extends BaseConfigDstu3Plus {
 	}
 
 	@Bean
-	public TransactionProcessor<Bundle, Bundle.BundleEntryComponent> transactionProcessor() {
+	public TransactionProcessor transactionProcessor() {
-		return new TransactionProcessor<>();
+		return new TransactionProcessor();
 	}
 
 	@Bean(name = GRAPHQL_PROVIDER_NAME)
@@ -142,11 +139,6 @@ public class BaseR4Config extends BaseConfigDstu3Plus {
 		return new SearchParamExtractorR4();
 	}
 
-	@Bean
-	public ISearchParamRegistry searchParamRegistry() {
-		return new SearchParamRegistryR4();
-	}
-
 	@Bean(name = "mySystemDaoR4", autowire = Autowire.BY_NAME)
 	public IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDaoR4() {
 		ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4 retVal = new ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4();

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

@@ -10,8 +10,6 @@ import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.r5.TransactionProcessorVersionAdapterR5;
 import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR5;
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR5;
 import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.jpa.term.TermReadSvcR5;
 import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcR5;
@@ -88,8 +86,8 @@ public class BaseR5Config extends BaseConfigDstu3Plus {
 	}
 
 	@Bean
-	public TransactionProcessor<Bundle, Bundle.BundleEntryComponent> transactionProcessor() {
+	public TransactionProcessor transactionProcessor() {
-		return new TransactionProcessor<>();
+		return new TransactionProcessor();
 	}
 
 	@Bean(name = GRAPHQL_PROVIDER_NAME)
@@ -142,11 +140,6 @@ public class BaseR5Config extends BaseConfigDstu3Plus {
 		return new SearchParamExtractorR5();
 	}
 
-	@Bean
-	public ISearchParamRegistry searchParamRegistry() {
-		return new SearchParamRegistryR5();
-	}
-
 	@Bean(name = "mySystemDaoR5", autowire = Autowire.BY_NAME)
 	public IFhirSystemDao<Bundle, org.hl7.fhir.r5.model.Meta> systemDaoR5() {
 		ca.uhn.fhir.jpa.dao.r5.FhirSystemDaoR5 retVal = new ca.uhn.fhir.jpa.dao.r5.FhirSystemDaoR5();

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

@@ -1,10 +1,21 @@
 package ca.uhn.fhir.jpa.dao;
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
-import ca.uhn.fhir.jpa.dao.data.*;
+import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceProvenanceDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
 import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
 import ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
@@ -13,6 +24,7 @@ import ca.uhn.fhir.jpa.delete.DeleteConflictService;
 import ca.uhn.fhir.jpa.entity.ResourceSearchView;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.*;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
@@ -74,7 +86,11 @@ import org.springframework.transaction.support.TransactionSynchronizationAdapter
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 
 import javax.annotation.PostConstruct;
-import javax.persistence.*;
+import javax.persistence.EntityManager;
+import javax.persistence.NoResultException;
+import javax.persistence.PersistenceContext;
+import javax.persistence.PersistenceContextType;
+import javax.persistence.TypedQuery;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Root;
@@ -83,7 +99,12 @@ import javax.xml.stream.events.XMLEvent;
 import java.util.*;
 import java.util.Map.Entry;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.left;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 /*
  * #%L
@@ -107,7 +128,7 @@ import static org.apache.commons.lang3.StringUtils.*;
 
 @SuppressWarnings("WeakerAccess")
 @Repository
-public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao, IJpaDao<T>, ApplicationContextAware {
+public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStorageDao implements IDao, IJpaDao<T>, ApplicationContextAware {
 
 	public static final long INDEX_STATUS_INDEXED = 1L;
 	public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
@@ -168,6 +189,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	private FhirContext myContext;
 	private ApplicationContext myApplicationContext;
 
+	@Override
+	protected IInterceptorBroadcaster getInterceptorBroadcaster() {
+		return myInterceptorBroadcaster;
+	}
+
 	protected ApplicationContext getApplicationContext() {
 		return myApplicationContext;
 	}
@@ -290,6 +316,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return retVal;
 	}
 
+	@Override
 	protected DaoConfig getConfig() {
 		return myConfig;
 	}
@@ -925,34 +952,36 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
+	public ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, IBasePersistedResource
 		theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		Validate.notNull(theEntity);
-		Validate.isTrue(theDeletedTimestampOrNull != null || theResource != null, "Must have either a resource[%s] or a deleted timestamp[%s] for resource PID[%s]", theDeletedTimestampOrNull != null, theResource != null, theEntity.getId());
+		Validate.isTrue(theDeletedTimestampOrNull != null || theResource != null, "Must have either a resource[%s] or a deleted timestamp[%s] for resource PID[%s]", theDeletedTimestampOrNull != null, theResource != null, theEntity.getPersistentId());
 
 		ourLog.debug("Starting entity update");
 
+		ResourceTable entity = (ResourceTable) theEntity;
+
 		/*
 		 * This should be the very first thing..
 		 */
 		if (theResource != null) {
 			if (thePerformIndexing) {
 				if (!ourValidationDisabledForUnitTest) {
-					validateResourceForStorage((T) theResource, theEntity);
+					validateResourceForStorage((T) theResource, entity);
 				}
 			}
 			String resourceType = myContext.getResourceDefinition(theResource).getName();
-			if (isNotBlank(theEntity.getResourceType()) && !theEntity.getResourceType().equals(resourceType)) {
+			if (isNotBlank(entity.getResourceType()) && !entity.getResourceType().equals(resourceType)) {
 				throw new UnprocessableEntityException(
-					"Existing resource ID[" + theEntity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + theEntity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
+					"Existing resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + entity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
 			}
 		}
 
-		if (theEntity.getPublished() == null) {
+		if (entity.getPublished() == null) {
 			ourLog.debug("Entity has published time: {}", new InstantDt(theUpdateTime));
 
-			theEntity.setPublished(theUpdateTime);
+			entity.setPublished(theUpdateTime);
 		}
 
 		ResourceIndexedSearchParams existingParams = null;
@@ -963,89 +992,89 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		if (theDeletedTimestampOrNull != null) {
 			// DELETE
 
-			theEntity.setDeleted(theDeletedTimestampOrNull);
+			entity.setDeleted(theDeletedTimestampOrNull);
-			theEntity.setUpdated(theDeletedTimestampOrNull);
+			entity.setUpdated(theDeletedTimestampOrNull);
-			theEntity.setNarrativeTextParsedIntoWords(null);
+			entity.setNarrativeTextParsedIntoWords(null);
-			theEntity.setContentTextParsedIntoWords(null);
+			entity.setContentTextParsedIntoWords(null);
-			theEntity.setHashSha256(null);
+			entity.setHashSha256(null);
-			theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
+			entity.setIndexStatus(INDEX_STATUS_INDEXED);
-			changed = populateResourceIntoEntity(theRequest, theResource, theEntity, true);
+			changed = populateResourceIntoEntity(theRequest, theResource, entity, true);
 
 		} else {
 			// CREATE or UPDATE
-			existingParams = new ResourceIndexedSearchParams(theEntity);
+			existingParams = new ResourceIndexedSearchParams(entity);
-			theEntity.setDeleted(null);
+			entity.setDeleted(null);
 
 			if (thePerformIndexing) {
 
 				newParams = new ResourceIndexedSearchParams();
-				mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theUpdateTime, theEntity, theResource, existingParams, theRequest);
+				mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theUpdateTime, entity, theResource, existingParams, theRequest);
 
-				changed = populateResourceIntoEntity(theRequest, theResource, theEntity, true);
+				changed = populateResourceIntoEntity(theRequest, theResource, entity, true);
 				if (changed.isChanged()) {
-					theEntity.setUpdated(theUpdateTime);
+					entity.setUpdated(theUpdateTime);
 					if (theResource instanceof IResource) {
-						theEntity.setLanguage(((IResource) theResource).getLanguage().getValue());
+						entity.setLanguage(((IResource) theResource).getLanguage().getValue());
 					} else {
-						theEntity.setLanguage(((IAnyResource) theResource).getLanguageElement().getValue());
+						entity.setLanguage(((IAnyResource) theResource).getLanguageElement().getValue());
 					}
 
-					newParams.setParamsOn(theEntity);
+					newParams.setParamsOn(entity);
-					theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
+					entity.setIndexStatus(INDEX_STATUS_INDEXED);
-					populateFullTextFields(myContext, theResource, theEntity);
+					populateFullTextFields(myContext, theResource, entity);
 				}
 			} else {
 
-				changed = populateResourceIntoEntity(theRequest, theResource, theEntity, false);
+				changed = populateResourceIntoEntity(theRequest, theResource, entity, false);
 
-				theEntity.setUpdated(theUpdateTime);
+				entity.setUpdated(theUpdateTime);
-				theEntity.setIndexStatus(null);
+				entity.setIndexStatus(null);
 
 			}
 
 		}
 
 		if (!changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
-			ourLog.debug("Resource {} has not changed", theEntity.getIdDt().toUnqualified().getValue());
+			ourLog.debug("Resource {} has not changed", entity.getIdDt().toUnqualified().getValue());
 			if (theResource != null) {
-				updateResourceMetadata(theEntity, theResource);
+				updateResourceMetadata(entity, theResource);
 			}
-			theEntity.setUnchangedInCurrentOperation(true);
+			entity.setUnchangedInCurrentOperation(true);
-			return theEntity;
+			return entity;
 		}
 
 		if (theUpdateVersion) {
-			theEntity.setVersion(theEntity.getVersion() + 1);
+			entity.setVersion(entity.getVersion() + 1);
 		}
 
 		/*
 		 * Save the resource itself
 		 */
-		if (theEntity.getId() == null) {
+		if (entity.getId() == null) {
-			myEntityManager.persist(theEntity);
+			myEntityManager.persist(entity);
 
-			if (theEntity.getForcedId() != null) {
+			if (entity.getForcedId() != null) {
-				myEntityManager.persist(theEntity.getForcedId());
+				myEntityManager.persist(entity.getForcedId());
 			}
 
-			postPersist(theEntity, (T) theResource);
+			postPersist(entity, (T) theResource);
 
-		} else if (theEntity.getDeleted() != null) {
+		} else if (entity.getDeleted() != null) {
-			theEntity = myEntityManager.merge(theEntity);
+			entity = myEntityManager.merge(entity);
 
-			postDelete(theEntity);
+			postDelete(entity);
 
 		} else {
-			theEntity = myEntityManager.merge(theEntity);
+			entity = myEntityManager.merge(entity);
 
-			postUpdate(theEntity, (T) theResource);
+			postUpdate(entity, (T) theResource);
 		}
 
 		/*
 		 * Create history entry
 		 */
 		if (theCreateNewHistoryEntry) {
-			final ResourceHistoryTable historyEntry = theEntity.toHistory();
+			final ResourceHistoryTable historyEntry = entity.toHistory();
 			historyEntry.setEncoding(changed.getEncoding());
 			historyEntry.setResource(changed.getResource());
 
@@ -1076,7 +1105,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			if (haveSource || haveRequestId) {
 				ResourceHistoryProvenanceEntity provenance = new ResourceHistoryProvenanceEntity();
 				provenance.setResourceHistoryTable(historyEntry);
-				provenance.setResourceTable(theEntity);
+				provenance.setResourceTable(entity);
 				if (haveRequestId) {
 					provenance.setRequestId(left(requestId, Constants.REQUEST_ID_LENGTH));
 				}
@@ -1102,7 +1131,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			for (String nextKey : newParams.getPopulatedResourceLinkParameters()) {
 				presentSearchParams.put(nextKey, Boolean.TRUE);
 			}
-			Set<Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();
+			Set<Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(entity.getResourceType()).entrySet();
 			for (Entry<String, RuntimeSearchParam> nextSpEntry : activeSearchParams) {
 				if (nextSpEntry.getValue().getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
 					if (!presentSearchParams.containsKey(nextSpEntry.getKey())) {
@@ -1110,13 +1139,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 					}
 				}
 			}
-			AddRemoveCount presenceCount = mySearchParamPresenceSvc.updatePresence(theEntity, presentSearchParams);
+			AddRemoveCount presenceCount = mySearchParamPresenceSvc.updatePresence(entity, presentSearchParams);
 
 			// Interceptor broadcast: JPA_PERFTRACE_INFO
 			if (!presenceCount.isEmpty()) {
 				if (JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequest)) {
 					StorageProcessingMessage message = new StorageProcessingMessage();
-					message.setMessage("For " + theEntity.getIdDt().toUnqualifiedVersionless().getValue() + " added " + presenceCount.getAddCount() + " and removed " + presenceCount.getRemoveCount() + " resource search parameter presence entries");
+					message.setMessage("For " + entity.getIdDt().toUnqualifiedVersionless().getValue() + " added " + presenceCount.getAddCount() + " and removed " + presenceCount.getRemoveCount() + " resource search parameter presence entries");
 					HookParams params = new HookParams()
 						.add(RequestDetails.class, theRequest)
 						.addIfMatchesType(ServletRequestDetails.class, theRequest)
@@ -1132,17 +1161,17 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		 */
 		if (thePerformIndexing) {
 			if (newParams == null) {
-				myExpungeService.deleteAllSearchParams(theEntity.getId());
+				myExpungeService.deleteAllSearchParams(entity.getId());
 			} else {
 
 				// Synchronize search param indexes
-				AddRemoveCount searchParamAddRemoveCount = myDaoSearchParamSynchronizer.synchronizeSearchParamsToDatabase(newParams, theEntity, existingParams);
+				AddRemoveCount searchParamAddRemoveCount = myDaoSearchParamSynchronizer.synchronizeSearchParamsToDatabase(newParams, entity, existingParams);
 
 				// Interceptor broadcast: JPA_PERFTRACE_INFO
 				if (!searchParamAddRemoveCount.isEmpty()) {
 					if (JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequest)) {
 						StorageProcessingMessage message = new StorageProcessingMessage();
-						message.setMessage("For " + theEntity.getIdDt().toUnqualifiedVersionless().getValue() + " added " + searchParamAddRemoveCount.getAddCount() + " and removed " + searchParamAddRemoveCount.getRemoveCount() + " resource search parameter index entries");
+						message.setMessage("For " + entity.getIdDt().toUnqualifiedVersionless().getValue() + " added " + searchParamAddRemoveCount.getAddCount() + " and removed " + searchParamAddRemoveCount.getRemoveCount() + " resource search parameter index entries");
 						HookParams params = new HookParams()
 							.add(RequestDetails.class, theRequest)
 							.addIfMatchesType(ServletRequestDetails.class, theRequest)
@@ -1152,25 +1181,27 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 				}
 
 				// Syncrhonize composite params
-				mySearchParamWithInlineReferencesExtractor.storeCompositeStringUniques(newParams, theEntity, existingParams);
+				mySearchParamWithInlineReferencesExtractor.storeCompositeStringUniques(newParams, entity, existingParams);
 			}
 		}
 
 		if (theResource != null) {
-			updateResourceMetadata(theEntity, theResource);
+			updateResourceMetadata(entity, theResource);
 		}
 
 
-		return theEntity;
+		return entity;
 	}
 
 	@Override
 	public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
-													ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource) {
+													IBasePersistedResource theEntity2, IIdType theResourceId, IBaseResource theOldResource) {
+
+		ResourceTable entity = (ResourceTable) theEntity2;
 
 		// We'll update the resource ID with the correct version later but for
 		// now at least set it to something useful for the interceptors
-		theResource.setId(theEntity.getIdDt());
+		theResource.setId(entity.getIdDt());
 
 		// Notify interceptors
 		ActionRequestDetails requestDetails;
@@ -1188,7 +1219,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		doCallHooks(theRequestDetails, Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, hookParams);
 
 		// Perform update
-		ResourceTable savedEntity = updateEntity(theRequestDetails, theResource, theEntity, null, thePerformIndexing, thePerformIndexing, new Date(), theForceUpdateVersion, thePerformIndexing);
+		ResourceTable savedEntity = updateEntity(theRequestDetails, 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),
@@ -1226,18 +1257,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return savedEntity;
 	}
 
-	protected void addPidToResource(ResourceTable theEntity, IBaseResource theResource) {
+	protected void addPidToResource(IBasePersistedResource theEntity, IBaseResource theResource) {
 		if (theResource instanceof IAnyResource) {
-			IDao.RESOURCE_PID.put((IAnyResource) theResource, theEntity.getId());
+			IDao.RESOURCE_PID.put((IAnyResource) theResource, theEntity.getPersistentId().getIdAsLong());
 		} else if (theResource instanceof IResource) {
-			IDao.RESOURCE_PID.put((IResource) theResource, theEntity.getId());
+			IDao.RESOURCE_PID.put((IResource) theResource, theEntity.getPersistentId().getIdAsLong());
 		}
 	}
 
-	protected void doCallHooks(RequestDetails theRequestDetails, Pointcut thePointcut, HookParams theParams) {
-		JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, thePointcut, theParams);
-	}
-
 	protected void updateResourceMetadata(IBaseResourceEntity theEntity, IBaseResource theResource) {
 		IIdType id = theEntity.getIdDt();
 		if (getContext().getVersion().getVersion().isRi()) {

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

@@ -26,7 +26,15 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.delete.DeleteConflictList;
-import ca.uhn.fhir.jpa.model.entity.*;
+import ca.uhn.fhir.jpa.delete.DeleteConflictService;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
+import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.model.entity.BaseTag;
+import ca.uhn.fhir.jpa.model.entity.ForcedId;
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.entity.TagDefinition;
+import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
@@ -40,22 +48,50 @@ import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.api.CacheControlDirective;
-import ca.uhn.fhir.rest.api.server.*;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PatchTypeEnum;
+import ca.uhn.fhir.rest.api.QualifiedParamList;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.api.ValidationModeEnum;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
+import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
+import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import ca.uhn.fhir.rest.param.QualifierDetails;
-import ca.uhn.fhir.rest.server.exceptions.*;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
-import ca.uhn.fhir.util.*;
+import ca.uhn.fhir.util.ObjectUtil;
-import ca.uhn.fhir.validation.*;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
+import ca.uhn.fhir.util.ReflectionUtil;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.IInstanceValidatorModule;
+import ca.uhn.fhir.validation.IValidationContext;
+import ca.uhn.fhir.validation.IValidatorModule;
+import ca.uhn.fhir.validation.ValidationOptions;
+import ca.uhn.fhir.validation.ValidationResult;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
-import org.hl7.fhir.r4.model.InstantType;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Required;
-import org.springframework.context.ApplicationContext;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.annotation.Propagation;
@@ -64,12 +100,10 @@ import org.springframework.transaction.support.TransactionSynchronizationAdapter
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
 import javax.persistence.TypedQuery;
 import javax.servlet.http.HttpServletResponse;
-import javax.validation.constraints.NotNull;
 import java.io.IOException;
 import java.util.*;
 
@@ -168,24 +202,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return create(theResource, theIfNoneExist, true, new Date(), theRequestDetails);
 	}
 
-	public IBaseOperationOutcome createErrorOperationOutcome(String theMessage, String theCode) {
-		return createOperationOutcome(OO_SEVERITY_ERROR, theMessage, theCode);
-	}
-
-	public IBaseOperationOutcome createInfoOperationOutcome(String theMessage) {
-		return createOperationOutcome(OO_SEVERITY_INFO, theMessage, "informational");
-	}
-
 	private IInstanceValidatorModule getInstanceValidator() {
 		return myInstanceValidator;
 	}
 
-	private IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
-		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
-		OperationOutcomeUtil.addIssue(getContext(), oo, theSeverity, theMessage, null, theCode);
-		return oo;
-	}
-
 	@Override
 	public DaoMethodOutcome delete(IIdType theId) {
 		return delete(theId, null);
@@ -281,7 +301,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		DaoMethodOutcome retVal = delete(theId, deleteConflicts, theRequestDetails);
 
-		myDeleteConflictService.validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
+		DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
 
 		ourLog.debug("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
 		return retVal;
@@ -295,7 +315,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	public DeleteMethodOutcome deleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequest) {
 		StopWatch w = new StopWatch();
 
-		Set<Long> resourceIds = myMatchResourceUrlService.processMatchUrl(theUrl, myResourceType, theRequest);
+		Set<ResourcePersistentId> resourceIds = myMatchResourceUrlService.processMatchUrl(theUrl, myResourceType, theRequest);
 		if (resourceIds.size() > 1) {
 			if (myDaoConfig.isAllowMultipleDelete() == false) {
 				throw new PreconditionFailedException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resourceIds.size()));
@@ -303,8 +323,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		List<ResourceTable> deletedResources = new ArrayList<>();
-		for (Long pid : resourceIds) {
+		for (ResourcePersistentId pid : resourceIds) {
-			ResourceTable entity = myEntityManager.find(ResourceTable.class, pid);
+			ResourceTable entity = myEntityManager.find(ResourceTable.class, pid.getId());
 			deletedResources.add(entity);
 
 			T resourceToDelete = toResource(myResourceType, entity, null, false);
@@ -372,7 +392,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequestDetails);
 
-		myDeleteConflictService.validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
+		DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
 
 		return outcome;
 	}
@@ -399,13 +419,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		entity.setResourceType(toResourceName(theResource));
 
 		if (isNotBlank(theIfNoneExist)) {
-			Set<Long> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theRequest);
+			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theRequest);
 			if (match.size() > 1) {
 				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
 				throw new PreconditionFailedException(msg);
 			} else if (match.size() == 1) {
-				Long pid = match.iterator().next();
+				ResourcePersistentId pid = match.iterator().next();
-				entity = myEntityManager.find(ResourceTable.class, pid);
+				entity = myEntityManager.find(ResourceTable.class, pid.getId());
 				IBaseResource resource = toResource(entity, false);
 				theResource.setId(resource.getIdElement().getValue());
 				return toMethodOutcome(theRequest, entity, resource).setCreated(false);
@@ -605,6 +625,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return myExpungeService.expunge(getResourceName(), null, null, theExpungeOptions, theRequestDetails);
 	}
 
+	@Override
 	public String getResourceName() {
 		return myResourceName;
 	}
@@ -790,13 +811,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		ResourceTable entityToUpdate;
 		if (isNotBlank(theConditionalUrl)) {
 
-			Set<Long> match = myMatchResourceUrlService.processMatchUrl(theConditionalUrl, myResourceType, theRequest);
+			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theConditionalUrl, myResourceType, theRequest);
 			if (match.size() > 1) {
 				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "PATCH", theConditionalUrl, match.size());
 				throw new PreconditionFailedException(msg);
 			} else if (match.size() == 1) {
-				Long pid = match.iterator().next();
+				ResourcePersistentId pid = match.iterator().next();
-				entityToUpdate = myEntityManager.find(ResourceTable.class, pid);
+				entityToUpdate = myEntityManager.find(ResourceTable.class, pid.getId());
 			} else {
 				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", theConditionalUrl);
 				throw new ResourceNotFoundException(msg);
@@ -848,57 +869,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		// nothing by default
 	}
 
-	/**
-	 * May be overridden by subclasses to validate resources prior to storage
-	 *
-	 * @param theResource The resource that is about to be stored
-	 */
-	protected void preProcessResourceForStorage(T theResource) {
-		String type = getContext().getResourceDefinition(theResource).getName();
-		if (!getResourceName().equals(type)) {
-			throw new InvalidRequestException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "incorrectResourceType", type, getResourceName()));
-		}
-
-		if (theResource.getIdElement().hasIdPart()) {
-			if (!theResource.getIdElement().isIdPartValid()) {
-				throw new InvalidRequestException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "failedToCreateWithInvalidId", theResource.getIdElement().getIdPart()));
-			}
-		}
-
-		/*
-		 * Replace absolute references with relative ones if configured to do so
-		 */
-		if (getConfig().getTreatBaseUrlsAsLocal().isEmpty() == false) {
-			FhirTerser t = getContext().newTerser();
-			List<ResourceReferenceInfo> refs = t.getAllResourceReferences(theResource);
-			for (ResourceReferenceInfo nextRef : refs) {
-				IIdType refId = nextRef.getResourceReference().getReferenceElement();
-				if (refId != null && refId.hasBaseUrl()) {
-					if (getConfig().getTreatBaseUrlsAsLocal().contains(refId.getBaseUrl())) {
-						IIdType newRefId = refId.toUnqualified();
-						nextRef.getResourceReference().setReference(newRefId.getValue());
-					}
-				}
-			}
-		}
-
-	}
-
 	@Override
-	public Set<Long> processMatchUrl(String theMatchUrl, RequestDetails theRequest) {
+	public IBaseResource readByPid(ResourcePersistentId thePid) {
-		return myMatchResourceUrlService.processMatchUrl(theMatchUrl, getResourceType(), theRequest);
-	}
-
-	@Override
-	public IBaseResource readByPid(Long thePid) {
 		StopWatch w = new StopWatch();
 
-		Optional<ResourceTable> entity = myResourceTableDao.findById(thePid);
+		Optional<ResourceTable> entity = myResourceTableDao.findById(thePid.getIdAsLong());
 		if (!entity.isPresent()) {
 			throw new ResourceNotFoundException("No resource found with PID " + thePid);
 		}
 		if (entity.get().getDeleted() != null) {
-			throw newResourceGoneException(entity.get());
+			throw createResourceGoneException(entity.get());
 		}
 
 		T retVal = toResource(myResourceType, entity.get(), null, false);
@@ -907,17 +887,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
-	@NotNull
-	private ResourceGoneException newResourceGoneException(BaseHasResource theResourceEntity) {
-		StringBuilder b = new StringBuilder();
-		b.append("Resource was deleted at ");
-		b.append(new InstantType(theResourceEntity.getDeleted()).getValueAsString());
-		ResourceGoneException retVal = new ResourceGoneException(b.toString());
-		retVal.setResourceId(theResourceEntity.getIdDt());
-		return retVal;
-	}
-
-
 	@Override
 	public T read(IIdType theId) {
 		return read(theId, null);
@@ -947,7 +916,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		if (theDeletedOk == false) {
 			if (entity.getDeleted() != null) {
-				throw newResourceGoneException(entity);
+				throw createResourceGoneException(entity);
 			}
 		}
 
@@ -990,8 +959,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	public BaseHasResource readEntity(IIdType theId, boolean theCheckForForcedId, RequestDetails theRequest) {
 		validateResourceTypeAndThrowInvalidRequestException(theId);
 
-		Long pid = myIdHelperService.translateForcedIdToPid(getResourceName(), theId.getIdPart(), theRequest);
+		ResourcePersistentId pid = myIdHelperService.translateForcedIdToPid(getResourceName(), theId.getIdPart(), theRequest);
-		BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid);
+		BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid.getIdAsLong());
 
 		if (entity == null) {
 			throw new ResourceNotFoundException(theId);
@@ -1009,7 +978,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		if (entity == null) {
 			if (theId.hasVersionIdPart()) {
 				TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery("SELECT t from ResourceHistoryTable t WHERE t.myResourceId = :RID AND t.myResourceType = :RTYP AND t.myResourceVersion = :RVER", ResourceHistoryTable.class);
-				q.setParameter("RID", pid);
+				q.setParameter("RID", pid.getId());
 				q.setParameter("RTYP", myResourceName);
 				q.setParameter("RVER", theId.getVersionIdPartAsLong());
 				try {
@@ -1029,7 +998,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	protected ResourceTable readEntityLatestVersion(IIdType theId, RequestDetails theRequest) {
-		ResourceTable entity = myEntityManager.find(ResourceTable.class, myIdHelperService.translateForcedIdToPid(getResourceName(), theId.getIdPart(), theRequest));
+		ResourcePersistentId persistentId = myIdHelperService.translateForcedIdToPid(getResourceName(), theId.getIdPart(), theRequest);
+		ResourceTable entity = myEntityManager.find(ResourceTable.class, persistentId.getId());
 		if (entity == null) {
 			throw new ResourceNotFoundException(theId);
 		}
@@ -1154,14 +1124,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
-	public Set<Long> searchForIds(SearchParameterMap theParams, RequestDetails theRequest) {
+	public Set<ResourcePersistentId> searchForIds(SearchParameterMap theParams, RequestDetails theRequest) {
 
 		SearchBuilder builder = newSearchBuilder();
 		builder.setType(getResourceType(), getResourceName());
 
 		// FIXME: fail if too many results
 
-		HashSet<Long> retVal = new HashSet<>();
+		HashSet<ResourcePersistentId> retVal = new HashSet<>();
 
 		String uuid = UUID.randomUUID().toString();
 		SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
@@ -1178,12 +1148,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) {
-		MT retVal;
+		MT retVal = ReflectionUtil.newInstance(theType);
-		try {
-			retVal = theType.newInstance();
-		} catch (Exception e) {
-			throw new InternalErrorException("Failed to instantiate " + theType.getName(), e);
-		}
 		for (TagDefinition next : tagDefinitions) {
 			switch (next.getTagType()) {
 				case PROFILE:
@@ -1200,58 +1165,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
-	private DaoMethodOutcome toMethodOutcome(RequestDetails theRequest, @Nonnull final ResourceTable theEntity, @Nonnull IBaseResource theResource) {
-		DaoMethodOutcome outcome = new DaoMethodOutcome();
-
-		IIdType id = null;
-		if (theResource.getIdElement().getValue() != null) {
-			id = theResource.getIdElement();
-		}
-		if (id == null) {
-			id = theEntity.getIdDt();
-			if (getContext().getVersion().getVersion().isRi()) {
-				id = getContext().getVersion().newIdType().setValue(id.getValue());
-			}
-		}
-
-		outcome.setId(id);
-		if (theEntity.getDeleted() == null) {
-			outcome.setResource(theResource);
-		}
-		outcome.setEntity(theEntity);
-
-		// Interceptor broadcast: STORAGE_PREACCESS_RESOURCES
-		if (outcome.getResource() != null) {
-			SimplePreResourceAccessDetails accessDetails = new SimplePreResourceAccessDetails(outcome.getResource());
-			HookParams params = new HookParams()
-				.add(IPreResourceAccessDetails.class, accessDetails)
-				.add(RequestDetails.class, theRequest)
-				.addIfMatchesType(ServletRequestDetails.class, theRequest);
-			JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PREACCESS_RESOURCES, params);
-			if (accessDetails.isDontReturnResourceAtIndex(0)) {
-				outcome.setResource(null);
-			}
-		}
-
-		// Interceptor broadcast: STORAGE_PRESHOW_RESOURCES
-		// Note that this will only fire if someone actually goes to use the
-		// resource in a response (it's their responsibility to call
-		// outcome.fireResourceViewCallback())
-		outcome.registerResourceViewCallback(() -> {
-			if (outcome.getResource() != null) {
-				SimplePreResourceShowDetails showDetails = new SimplePreResourceShowDetails(outcome.getResource());
-				HookParams params = new HookParams()
-					.add(IPreResourceShowDetails.class, showDetails)
-					.add(RequestDetails.class, theRequest)
-					.addIfMatchesType(ServletRequestDetails.class, theRequest);
-				JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PRESHOW_RESOURCES, params);
-				outcome.setResource(showDetails.getResource(0));
-			}
-		});
-
-		return outcome;
-	}
-
 	private ArrayList<TagDefinition> toTagList(IBaseMetaType theMeta) {
 		ArrayList<TagDefinition> retVal = new ArrayList<>();
 
@@ -1340,13 +1253,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		IIdType resourceId;
 		if (isNotBlank(theMatchUrl)) {
-			Set<Long> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theRequest);
+			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theRequest);
 			if (match.size() > 1) {
 				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size());
 				throw new PreconditionFailedException(msg);
 			} else if (match.size() == 1) {
-				Long pid = match.iterator().next();
+				ResourcePersistentId pid = match.iterator().next();
-				entity = myEntityManager.find(ResourceTable.class, pid);
+				entity = myEntityManager.find(ResourceTable.class, pid.getId());
 				resourceId = entity.getIdDt();
 			} else {
 				return create(theResource, null, thePerformIndexing, new Date(), theRequest);
@@ -1440,7 +1353,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			if (myDaoConfig.isEnforceReferentialIntegrityOnDelete()) {
 				myDeleteConflictService.validateOkToDelete(deleteConflicts, entity, true, theRequest);
 			}
-			myDeleteConflictService.validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
+			DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
 
 			IBaseOperationOutcome oo = createInfoOperationOutcome("Ok to delete");
 			return new MethodOutcome(new IdDt(theId.getValue()), oo);

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

@@ -88,4 +88,9 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 	}
 
 
+	@Nullable
+	@Override
+	protected String getResourceName() {
+		return null;
+	}
 }

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

@@ -0,0 +1,204 @@
+package ca.uhn.fhir.jpa.dao;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.api.HookParams;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
+import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
+import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
+import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.FhirTerser;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
+import ca.uhn.fhir.util.ResourceReferenceInfo;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.InstantType;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import javax.validation.constraints.NotNull;
+import java.util.List;
+import java.util.Set;
+
+import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR;
+import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public abstract class BaseStorageDao {
+
+	/**
+	 * May be overridden by subclasses to validate resources prior to storage
+	 *
+	 * @param theResource The resource that is about to be stored
+	 */
+	protected void preProcessResourceForStorage(IBaseResource theResource) {
+		String type = getContext().getResourceDefinition(theResource).getName();
+		if (getResourceName() != null && !getResourceName().equals(type)) {
+			throw new InvalidRequestException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "incorrectResourceType", type, getResourceName()));
+		}
+
+		if (theResource.getIdElement().hasIdPart()) {
+			if (!theResource.getIdElement().isIdPartValid()) {
+				throw new InvalidRequestException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "failedToCreateWithInvalidId", theResource.getIdElement().getIdPart()));
+			}
+		}
+
+		/*
+		 * Replace absolute references with relative ones if configured to do so
+		 */
+		if (getConfig().getTreatBaseUrlsAsLocal().isEmpty() == false) {
+			FhirTerser t = getContext().newTerser();
+			List<ResourceReferenceInfo> refs = t.getAllResourceReferences(theResource);
+			for (ResourceReferenceInfo nextRef : refs) {
+				IIdType refId = nextRef.getResourceReference().getReferenceElement();
+				if (refId != null && refId.hasBaseUrl()) {
+					if (getConfig().getTreatBaseUrlsAsLocal().contains(refId.getBaseUrl())) {
+						IIdType newRefId = refId.toUnqualified();
+						nextRef.getResourceReference().setReference(newRefId.getValue());
+					}
+				}
+			}
+		}
+
+		if ("Bundle".equals(type)) {
+			Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
+			String bundleType = BundleUtil.getBundleType(getContext(), (IBaseBundle) theResource);
+			if (isBlank(bundleType) || !allowedBundleTypes.contains(bundleType)) {
+				String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (isNotBlank(bundleType) ? bundleType : "(missing)");
+				throw new UnprocessableEntityException(message);
+			}
+		}
+
+	}
+
+	protected DaoMethodOutcome toMethodOutcome(RequestDetails theRequest, @Nonnull final IBasePersistedResource theEntity, @Nonnull IBaseResource theResource) {
+		DaoMethodOutcome outcome = new DaoMethodOutcome();
+
+		IIdType id = null;
+		if (theResource.getIdElement().getValue() != null) {
+			id = theResource.getIdElement();
+		}
+		if (id == null) {
+			id = theEntity.getIdDt();
+			if (getContext().getVersion().getVersion().isRi()) {
+				id = getContext().getVersion().newIdType().setValue(id.getValue());
+			}
+		}
+
+		outcome.setId(id);
+		if (theEntity.isDeleted() == false) {
+			outcome.setResource(theResource);
+		}
+		outcome.setEntity(theEntity);
+
+		// Interceptor broadcast: STORAGE_PREACCESS_RESOURCES
+		if (outcome.getResource() != null) {
+			SimplePreResourceAccessDetails accessDetails = new SimplePreResourceAccessDetails(outcome.getResource());
+			HookParams params = new HookParams()
+				.add(IPreResourceAccessDetails.class, accessDetails)
+				.add(RequestDetails.class, theRequest)
+				.addIfMatchesType(ServletRequestDetails.class, theRequest);
+			JpaInterceptorBroadcaster.doCallHooks(getInterceptorBroadcaster(), theRequest, Pointcut.STORAGE_PREACCESS_RESOURCES, params);
+			if (accessDetails.isDontReturnResourceAtIndex(0)) {
+				outcome.setResource(null);
+			}
+		}
+
+		// Interceptor broadcast: STORAGE_PRESHOW_RESOURCES
+		// Note that this will only fire if someone actually goes to use the
+		// resource in a response (it's their responsibility to call
+		// outcome.fireResourceViewCallback())
+		outcome.registerResourceViewCallback(() -> {
+			if (outcome.getResource() != null) {
+				SimplePreResourceShowDetails showDetails = new SimplePreResourceShowDetails(outcome.getResource());
+				HookParams params = new HookParams()
+					.add(IPreResourceShowDetails.class, showDetails)
+					.add(RequestDetails.class, theRequest)
+					.addIfMatchesType(ServletRequestDetails.class, theRequest);
+				JpaInterceptorBroadcaster.doCallHooks(getInterceptorBroadcaster(), theRequest, Pointcut.STORAGE_PRESHOW_RESOURCES, params);
+				outcome.setResource(showDetails.getResource(0));
+			}
+		});
+
+		return outcome;
+	}
+
+	protected void doCallHooks(RequestDetails theRequestDetails, Pointcut thePointcut, HookParams theParams) {
+		JpaInterceptorBroadcaster.doCallHooks(getInterceptorBroadcaster(), theRequestDetails, thePointcut, theParams);
+	}
+
+	protected abstract IInterceptorBroadcaster getInterceptorBroadcaster();
+
+	public IBaseOperationOutcome createErrorOperationOutcome(String theMessage, String theCode) {
+		return createOperationOutcome(OO_SEVERITY_ERROR, theMessage, theCode);
+	}
+
+	public IBaseOperationOutcome createInfoOperationOutcome(String theMessage) {
+		return createOperationOutcome(OO_SEVERITY_INFO, theMessage, "informational");
+	}
+
+	private IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
+		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
+		OperationOutcomeUtil.addIssue(getContext(), oo, theSeverity, theMessage, null, theCode);
+		return oo;
+	}
+
+	@NotNull
+	protected ResourceGoneException createResourceGoneException(IBasePersistedResource theResourceEntity) {
+		StringBuilder b = new StringBuilder();
+		b.append("Resource was deleted at ");
+		b.append(new InstantType(theResourceEntity.getDeleted()).getValueAsString());
+		ResourceGoneException retVal = new ResourceGoneException(b.toString());
+		retVal.setResourceId(theResourceEntity.getIdDt());
+		return retVal;
+	}
+
+	/**
+	 * Provide the DaoConfig
+	 */
+	protected abstract DaoConfig getConfig();
+
+	/**
+	 * Returns the resource type for this DAO, or null if this is a system-level DAO
+	 */
+	@Nullable
+	protected abstract String getResourceName();
+
+	/**
+	 * Provides the FHIR context
+	 */
+	protected abstract FhirContext getContext();
+
+}

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

@@ -20,13 +20,14 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.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 IBasePersistedResource myEntity;
 	private IBaseResource myPreviousResource;
 
 	/**
@@ -36,11 +37,11 @@ public class DaoMethodOutcome extends MethodOutcome {
 		super();
 	}
 
-	public ResourceTable getEntity() {
+	public IBasePersistedResource getEntity() {
 		return myEntity;
 	}
 
-	public DaoMethodOutcome setEntity(ResourceTable theEntity) {
+	public DaoMethodOutcome setEntity(IBasePersistedResource theEntity) {
 		myEntity = theEntity;
 		return this;
 	}

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

@@ -80,8 +80,7 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
 	 * @throws InvalidRequestException If the given resource type is not supported
 	 */
 	public IFhirResourceDao getResourceDao(String theResourceName) {
-		init();
+		IFhirResourceDao<IBaseResource> retVal = getResourceDaoOrNull(theResourceName);
-		IFhirResourceDao retVal = myResourceNameToResourceDao.get(theResourceName);
 		if (retVal == null) {
 			List<String> supportedResourceTypes = myResourceNameToResourceDao
 				.keySet()
@@ -126,12 +125,9 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
 	}
 
 	@Nullable
-	public <T extends IBaseResource> IFhirResourceDao<T> getResourceDaoOrNull(String theResourceType) {
+	public <T extends IBaseResource> IFhirResourceDao<T> getResourceDaoOrNull(String theResourceName) {
-		try {
+		init();
-			return (IFhirResourceDao<T>) getResourceDao(theResourceType);
+		return (IFhirResourceDao<T>) myResourceNameToResourceDao.get(theResourceName);
-		} catch (InvalidRequestException e) {
-			return null;
-		}
 	}
 
 	@Override

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

@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.dao;
  */
 
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.searchparam.registry.BaseSearchParamRegistry;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamProvider;
 import ca.uhn.fhir.model.dstu2.valueset.ResourceTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -44,7 +44,7 @@ public class DaoSearchParamProvider implements ISearchParamProvider {
 	}
 
 	@Override
-	public <SP extends IBaseResource> int refreshCache(BaseSearchParamRegistry<SP> theSearchParamRegistry, long theRefreshInterval) {
+	public int refreshCache(SearchParamRegistryImpl theSearchParamRegistry, long theRefreshInterval) {
 		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
 		return txTemplate.execute(t-> theSearchParamRegistry.doRefresh(theRefreshInterval));
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoBundleDstu2.java

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import java.util.Set;
 
@@ -31,16 +32,10 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 public class FhirResourceDaoBundleDstu2 extends BaseHapiFhirResourceDao<Bundle> {
 
 	@Override
-	protected void preProcessResourceForStorage(Bundle theResource) {
+	protected void preProcessResourceForStorage(IBaseResource theResource) {
 		super.preProcessResourceForStorage(theResource);
 
-		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
+		for (Entry next : ((Bundle)theResource).getEntry()) {
-		if (!allowedBundleTypes.contains(defaultString(theResource.getType()))) {
-			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType() : "(missing)");
-			throw new UnprocessableEntityException(message);
-		}
-
-		for (Entry next : theResource.getEntry()) {
 			next.setFullUrl((String) null);
 		}
 	}

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.SubscriptionTable;
 import ca.uhn.fhir.model.dstu2.resource.Subscription;
@@ -73,12 +74,12 @@ public class FhirResourceDaoSubscriptionDstu2 extends BaseHapiFhirResourceDao<Su
 
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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) {
-			mySubscriptionTableDao.deleteAllForSubscription(theEntity);
+			mySubscriptionTableDao.deleteAllForSubscription((ResourceTable) theEntity);
 		}
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
@@ -68,6 +69,8 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 	@Autowired
 	@Qualifier("myFhirContextDstu2Hl7Org")
 	private FhirContext myRiCtx;
+	@Autowired
+	private FhirContext myFhirContext;
 
 	private CachingValidationSupport myValidationSupport;
 
@@ -176,14 +179,15 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
 		if (theSystem != null && theSystem.startsWith("http://hl7.org/fhir/")) {
-			return Collections.singletonList((IIdType) new IdDt(theSystem));
+			return Collections.singletonList(new IdDt(theSystem));
 		}
 
 		List<IIdType> valueSetIds;
-		Set<Long> ids = searchForIds(new SearchParameterMap(ValueSet.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(ValueSet.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		valueSetIds = new ArrayList<IIdType>();
-		for (Long next : ids) {
+		for (ResourcePersistentId next : ids) {
-			valueSetIds.add(new IdDt("ValueSet", next));
+			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "ValueSet", next);
+			valueSetIds.add(id);
 		}
 		return valueSetIds;
 	}
@@ -309,10 +313,11 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
 		if (theId != null) {
 			valueSetIds = Collections.singletonList(theId);
 		} else if (haveIdentifierParam) {
-			Set<Long> ids = searchForIds(new SearchParameterMap(ValueSet.SP_IDENTIFIER, new TokenParam(null, theValueSetIdentifier.getValue())), theRequest);
+			Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(ValueSet.SP_IDENTIFIER, new TokenParam(null, theValueSetIdentifier.getValue())), theRequest);
 			valueSetIds = new ArrayList<>();
-			for (Long next : ids) {
+			for (ResourcePersistentId next : ids) {
-				valueSetIds.add(new IdDt("ValueSet", next));
+				IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "ValueSet", next);
+				valueSetIds.add(id);
 			}
 		} else {
 			if (theCode == null || theCode.isEmpty()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -22,6 +22,9 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.delete.DeleteConflictList;
+import ca.uhn.fhir.jpa.delete.DeleteConflictService;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.entity.TagDefinition;
 import ca.uhn.fhir.rest.server.servlet.ServletSubRequestDetails;
@@ -86,6 +89,8 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 	private MatchUrlService myMatchUrlService;
 	@Autowired
 	private DaoRegistry myDaoRegistry;
+	@Autowired
+	private MatchResourceUrlService myMatchResourceUrlService;
 
 	private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) {
 		ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size());
@@ -213,9 +218,9 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 		List<IIdType> deletedResources = new ArrayList<>();
 		DeleteConflictList deleteConflicts = new DeleteConflictList();
-		Map<Entry, ResourceTable> entriesToProcess = new IdentityHashMap<>();
+		Map<Entry, IBasePersistedResource> entriesToProcess = new IdentityHashMap<>();
-		Set<ResourceTable> nonUpdatedEntities = new HashSet<ResourceTable>();
+		Set<IBasePersistedResource> nonUpdatedEntities = new HashSet<>();
-		Set<ResourceTable> updatedEntities = new HashSet<>();
+		Set<IBasePersistedResource> updatedEntities = new HashSet<>();
 
 		/*
 		 * Handle: GET/PUT/POST
@@ -293,7 +298,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 		}
 
-		for (Map.Entry<Entry, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
+		for (Map.Entry<Entry, IBasePersistedResource> nextEntry : entriesToProcess.entrySet()) {
 			nextEntry.getKey().getResponse().setLocation(nextEntry.getValue().getIdDt().toUnqualified().getValue());
 			nextEntry.getKey().getResponse().setEtag(nextEntry.getValue().getIdDt().getVersionIdPart());
 		}
@@ -301,13 +306,13 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		long delay = System.currentTimeMillis() - start;
 		int numEntries = theRequest.getEntry().size();
 		long delayPer = delay / numEntries;
-		ourLog.info("{} completed in {}ms ({} entries at {}ms per entry)", new Object[] {theActionName, delay, numEntries, delayPer});
+		ourLog.info("{} completed in {}ms ({} entries at {}ms per entry)", theActionName, delay, numEntries, delayPer);
 
 		response.setType(BundleTypeEnum.TRANSACTION_RESPONSE);
 		return response;
 	}
 
-	private void handleTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date theUpdateTime, Set<IdDt> theAllIds, Map<IdDt, IdDt> theIdSubstitutions, Map<IdDt, DaoMethodOutcome> theIdToPersistedOutcome, Bundle theResponse, IdentityHashMap<Entry, Integer> theOriginalRequestOrder, List<IIdType> theDeletedResources, DeleteConflictList theDeleteConflicts, Map<Entry, ResourceTable> theEntriesToProcess, Set<ResourceTable> theNonUpdatedEntities, Set<ResourceTable> theUpdatedEntities) {
+	private void handleTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date theUpdateTime, Set<IdDt> theAllIds, Map<IdDt, IdDt> theIdSubstitutions, Map<IdDt, DaoMethodOutcome> theIdToPersistedOutcome, Bundle theResponse, IdentityHashMap<Entry, Integer> theOriginalRequestOrder, List<IIdType> theDeletedResources, DeleteConflictList theDeleteConflicts, Map<Entry, IBasePersistedResource> theEntriesToProcess, Set<IBasePersistedResource> theNonUpdatedEntities, Set<IBasePersistedResource> theUpdatedEntities) {
 		/*
 		 * Loop through the request and process any entries of type
 		 * PUT, POST or DELETE
@@ -331,7 +336,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 					}
 				}
 
-				if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*") && !isPlaceholder(nextResourceId)) {
+				if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+:.*") && !isPlaceholder(nextResourceId)) {
 					throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
 				}
 
@@ -444,7 +449,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		 */
 
 		theDeleteConflicts.removeIf(next -> theDeletedResources.contains(next.getTargetId().toVersionless()));
-		myDeleteConflictService.validateDeleteConflictsEmptyOrThrowException(theDeleteConflicts);
+		DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), theDeleteConflicts);
 
 		/*
 		 * Perform ID substitutions and then index each resource we have saved
@@ -508,8 +513,8 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 			if (nextEntry.getRequest().getMethodElement().getValueAsEnum() == HTTPVerbEnum.POST) {
 				String matchUrl = nextEntry.getRequest().getIfNoneExist();
 				if (isNotBlank(matchUrl)) {
-					IFhirResourceDao<?> resourceDao = getDao(nextEntry.getResource().getClass());
+					Class<? extends IBaseResource> resType = nextEntry.getResource().getClass();
-					Set<Long> val = resourceDao.processMatchUrl(matchUrl, theRequestDetails);
+					Set<ResourcePersistentId> val = myMatchResourceUrlService.processMatchUrl(matchUrl, resType, theRequestDetails);
 					if (val.size() > 1) {
 						throw new InvalidRequestException(
 							"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
@@ -623,11 +628,11 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 	}
 
 	private Bundle transaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
-		super.markRequestAsProcessingSubRequest(theRequestDetails);
+		markRequestAsProcessingSubRequest(theRequestDetails);
 		try {
 			return doTransaction(theRequestDetails, theRequest, theActionName);
 		} finally {
-			super.clearRequestAsProcessingSubRequest(theRequestDetails);
+			clearRequestAsProcessingSubRequest(theRequestDetails);
 		}
 	}
 
@@ -655,15 +660,13 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 	private static boolean isPlaceholder(IdDt theId) {
 		if (theId.getValue() != null) {
-			if (theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:")) {
+			return theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:");
-				return true;
-			}
 		}
 		return false;
 	}
 
 	private static String toStatusString(int theStatusCode) {
-		return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
+		return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
 	}
 
 	@Override

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -116,10 +117,10 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 		}
 	}
 
-	private List<Long> doSearch(String theResourceName, SearchParameterMap theParams, Long theReferencingPid) {
+	private List<ResourcePersistentId> doSearch(String theResourceName, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
 		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
 
-		List<Long> pids = null;
+		List<ResourcePersistentId> pids = null;
 		
 		/*
 		 * Handle textual params
@@ -202,12 +203,12 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 		// execute search
 		List<?> result = jpaQuery.getResultList();
 
-		ArrayList<Long> retVal = new ArrayList<>();
+		ArrayList<ResourcePersistentId> retVal = new ArrayList<>();
 		for (Object object : result) {
 			Object[] nextArray = (Object[]) object;
 			Long next = (Long) nextArray[0];
 			if (next != null) {
-				retVal.add(next);
+				retVal.add(new ResourcePersistentId(next));
 			}
 		}
 
@@ -215,9 +216,9 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 	}
 
 	@Override
-	public List<Long> everything(String theResourceName, SearchParameterMap theParams, RequestDetails theRequest) {
+	public List<ResourcePersistentId> everything(String theResourceName, SearchParameterMap theParams, RequestDetails theRequest) {
 
-		Long pid = null;
+		ResourcePersistentId pid = null;
 		if (theParams.get(IAnyResource.SP_RES_ID) != null) {
 			String idParamValue;
 			IQueryParameterType idParam = theParams.get(IAnyResource.SP_RES_ID).get(0).get(0);
@@ -231,8 +232,8 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 			pid = myIdHelperService.translateForcedIdToPid(theResourceName, idParamValue, theRequest);
 		}
 
-		Long referencingPid = pid;
+		ResourcePersistentId referencingPid = pid;
-		List<Long> retVal = doSearch(null, theParams, referencingPid);
+		List<ResourcePersistentId> retVal = doSearch(null, theParams, referencingPid);
 		if (referencingPid != null) {
 			retVal.add(referencingPid);
 		}
@@ -264,7 +265,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 
 	@Transactional()
 	@Override
-	public List<Long> search(String theResourceName, SearchParameterMap theParams) {
+	public List<ResourcePersistentId> search(String theResourceName, SearchParameterMap theParams) {
 		return doSearch(theResourceName, theParams, null);
 	}
 
@@ -281,7 +282,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 		if (contextParts.length != 3 || "Patient".equals(contextParts[0]) == false || "$everything".equals(contextParts[2]) == false) {
 			throw new InvalidRequestException("Invalid context: " + theContext);
 		}
-		Long pid = myIdHelperService.translateForcedIdToPid(contextParts[0], contextParts[1], theRequest);
+		ResourcePersistentId pid = myIdHelperService.translateForcedIdToPid(contextParts[0], contextParts[1], theRequest);
 
 		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
 

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

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.delete.DeleteConflictList;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
@@ -154,8 +155,6 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
 	DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails);
 
-	Set<Long> processMatchUrl(String theMatchUrl, RequestDetails theRequest);
-
 	/**
 	 * Read a resource - Note that this variant of the method does not take in a {@link RequestDetails} and
 	 * therefore can not fire any interceptors. Use only for internal system calls
@@ -165,7 +164,7 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	/**
 	 * Read a resource by its internal PID
 	 */
-	IBaseResource readByPid(Long thePid);
+	IBaseResource readByPid(ResourcePersistentId thePid);
 
 	/**
 	 * @param theId
@@ -205,7 +204,7 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	@Transactional(propagation = Propagation.SUPPORTS)
 	IBundleProvider search(SearchParameterMap theParams, RequestDetails theRequestDetails, HttpServletResponse theServletResponse);
 
-	Set<Long> searchForIds(SearchParameterMap theParams, RequestDetails theRequest);
+	Set<ResourcePersistentId> searchForIds(SearchParameterMap theParams, RequestDetails theRequest);
 
 	/**
 	 * Takes a map of incoming raw search parameters and translates/parses them into

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao;
 import java.util.List;
 
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 
@@ -30,9 +31,9 @@ public interface IFulltextSearchSvc {
 
 	List<Suggestion> suggestKeywords(String theContext, String theSearchParam, String theText, RequestDetails theRequest);
 	
-	List<Long> search(String theResourceName, SearchParameterMap theParams);
+	List<ResourcePersistentId> search(String theResourceName, SearchParameterMap theParams);
 
-	List<Long> everything(String theResourceName, SearchParameterMap theParams, RequestDetails theRequest);
+	List<ResourcePersistentId> everything(String theResourceName, SearchParameterMap theParams, RequestDetails theRequest);
 
 	boolean isDisabled();
 

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -29,10 +30,10 @@ import java.util.Date;
 
 public interface IJpaDao<T extends IBaseResource> {
 	@SuppressWarnings("unchecked")
-	ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable
+	IBasePersistedResource updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource
 		theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 										boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry);
 
-	ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
+	IBasePersistedResource updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
-										  ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource);
+										  IBasePersistedResource theEntity, IIdType theResourceId, IBaseResource theOldResource);
 }

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

@@ -20,10 +20,12 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
+
 import java.io.Closeable;
 import java.util.Iterator;
 
-public interface IResultIterator extends Iterator<Long>, Closeable {
+public interface IResultIterator extends Iterator<ResourcePersistentId>, Closeable {
 
 	int getSkippedCount();
 

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.Include;
@@ -43,9 +44,9 @@ public interface ISearchBuilder {
 
 	Iterator<Long> createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest);
 
-	void loadResourcesByPid(Collection<Long> thePids, Collection<Long> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation, RequestDetails theDetails);
+	void loadResourcesByPid(Collection<ResourcePersistentId> thePids, Collection<ResourcePersistentId> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation, RequestDetails theDetails);
 
-	Set<Long> loadIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
+	Set<ResourcePersistentId> loadIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<ResourcePersistentId> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
 								  DateRangeParam theLastUpdated, String theSearchIdOrDescription, RequestDetails theRequest);
 
 	/**
@@ -55,6 +56,6 @@ public interface ISearchBuilder {
 
 	void setType(Class<? extends IBaseResource> theResourceType, String theResourceName);
 
-	void setPreviouslyAddedResourcePids(List<Long> thePreviouslyAddedResourcePids);
+	void setPreviouslyAddedResourcePids(List<ResourcePersistentId> thePreviouslyAddedResourcePids);
 
 }

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

@@ -25,8 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
-import ca.uhn.fhir.jpa.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -37,7 +36,6 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.StopWatch;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Request;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -54,7 +52,7 @@ public class MatchResourceUrlService {
 	@Autowired
 	private IInterceptorBroadcaster myInterceptorBroadcaster;
 
-	public <R extends IBaseResource> Set<Long> processMatchUrl(String theMatchUrl, Class<R> theResourceType, RequestDetails theRequest) {
+	public <R extends IBaseResource> Set<ResourcePersistentId> processMatchUrl(String theMatchUrl, Class<R> theResourceType, RequestDetails theRequest) {
 		StopWatch sw = new StopWatch();
 
 		RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(theResourceType);
@@ -71,7 +69,7 @@ public class MatchResourceUrlService {
 			throw new InternalErrorException("No DAO for resource type: " + theResourceType.getName());
 		}
 
-		Set<Long> retVal = dao.searchForIds(paramMap, theRequest);
+		Set<ResourcePersistentId> retVal = dao.searchForIds(paramMap, theRequest);
 
 		// Interceptor broadcast: JPA_PERFTRACE_INFO
 		if (JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequest)) {

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

@@ -20,7 +20,15 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
-import ca.uhn.fhir.context.*;
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
+import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
@@ -30,6 +38,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.entity.ResourceSearchView;
 import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.*;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
@@ -40,10 +49,20 @@ import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.util.SourceParam;
-import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
-import ca.uhn.fhir.jpa.util.*;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
-import ca.uhn.fhir.model.api.*;
+import ca.uhn.fhir.jpa.util.BaseIterator;
+import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
+import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
+import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
+import ca.uhn.fhir.jpa.util.SqlQueryList;
+import ca.uhn.fhir.model.api.IPrimitiveDatatype;
+import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
 import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
@@ -51,7 +70,11 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.parser.DataFormatException;
-import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.QualifiedParamList;
+import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.api.SortOrderEnum;
+import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.*;
@@ -96,7 +119,11 @@ import java.util.Map.Entry;
 import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 /**
  * The SearchBuilder is responsible for actually forming the SQL query that handles
@@ -106,14 +133,14 @@ import static org.apache.commons.lang3.StringUtils.*;
 @Scope("prototype")
 public class SearchBuilder implements ISearchBuilder {
 
-	private static final List<Long> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
+	private static final List<ResourcePersistentId> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilder.class);
 	/**
 	 * See loadResourcesByPid
 	 * for an explanation of why we use the constant 800
 	 */
 	private static final int MAXIMUM_PAGE_SIZE = 800;
-	private static Long NO_MORE = -1L;
+	private static ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
 	private final boolean myDontUseHashesForSearch;
 	private final DaoConfig myDaoConfig;
 	@Autowired
@@ -138,7 +165,7 @@ public class SearchBuilder implements ISearchBuilder {
 	private ITermReadSvc myTerminologySvc;
 	@Autowired
 	private MatchUrlService myMatchUrlService;
-	private List<Long> myAlsoIncludePids;
+	private List<ResourcePersistentId> myAlsoIncludePids;
 	private CriteriaBuilder myBuilder;
 	private BaseHapiFhirDao<?> myCallingDao;
 	private Map<JoinKey, Join<?, ?>> myIndexJoins = Maps.newHashMap();
@@ -151,7 +178,7 @@ public class SearchBuilder implements ISearchBuilder {
 	private String mySearchUuid;
 	private int myFetchSize;
 	private Integer myMaxResultsToFetch;
-	private Set<Long> myPidSet;
+	private Set<ResourcePersistentId> myPidSet;
 	private boolean myHaveIndexJoins = false;
 
 	/**
@@ -542,11 +569,11 @@ public class SearchBuilder implements ISearchBuilder {
 		List<Predicate> codePredicates = new ArrayList<>();
 
 		// Resources by ID
-		List<Long> targetPids = myIdHelperService.translateForcedIdToPids(targetIds, theRequest);
+		List<ResourcePersistentId> targetPids = myIdHelperService.translateForcedIdToPids(targetIds, theRequest);
 		if (!targetPids.isEmpty()) {
 			ourLog.debug("Searching for resource link with target PIDs: {}", targetPids);
 			Predicate pathPredicate = createResourceLinkPathPredicate(theResourceName, theParamName, join);
-			Predicate pidPredicate = join.get("myTargetResourcePid").in(targetPids);
+			Predicate pidPredicate = join.get("myTargetResourcePid").in(ResourcePersistentId.toLongList(targetPids));
 			codePredicates.add(myBuilder.and(pathPredicate, pidPredicate));
 		}
 
@@ -573,7 +600,6 @@ public class SearchBuilder implements ISearchBuilder {
 
 	private Predicate addPredicateReferenceWithChain(String theResourceName, String theParamName, List<? extends IQueryParameterType> theList, Join<ResourceTable, ResourceLink> theJoin, List<Predicate> theCodePredicates, ReferenceParam theRef, RequestDetails theRequest) {
 		final List<Class<? extends IBaseResource>> resourceTypes;
-		String resourceId;
 		if (!theRef.hasResourceType()) {
 
 			RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
@@ -631,14 +657,11 @@ public class SearchBuilder implements ISearchBuilder {
 				}
 			}
 
-			resourceId = theRef.getValue();
-
 		} else {
 			try {
 				RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theRef.getResourceType());
 				resourceTypes = new ArrayList<>(1);
 				resourceTypes.add(resDef.getImplementingClass());
-				resourceId = theRef.getIdPart();
 			} catch (DataFormatException e) {
 				throw new InvalidRequestException("Invalid resource type: " + theRef.getResourceType());
 			}
@@ -712,6 +735,42 @@ public class SearchBuilder implements ISearchBuilder {
 		return predicate;
 	}
 
+	private void addPredicateSource(List<List<IQueryParameterType>> theAndOrParams, RequestDetails theRequest) {
+		for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
+			addPredicateSource(nextAnd, SearchFilterParser.CompareOperation.eq, theRequest);
+		}
+	}
+
+	private Predicate addPredicateSource(List<? extends IQueryParameterType> theList, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequest) {
+		if (myDaoConfig.getStoreMetaSourceInformation() == DaoConfig.StoreMetaSourceInformationEnum.NONE) {
+			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "sourceParamDisabled");
+			throw new InvalidRequestException(msg);
+		}
+
+		Join<ResourceTable, ResourceHistoryProvenanceEntity> join = myResourceTableRoot.join("myProvenance", JoinType.LEFT);
+
+		List<Predicate> codePredicates = new ArrayList<>();
+
+		for (IQueryParameterType nextParameter : theList) {
+			SourceParam sourceParameter = new SourceParam(nextParameter.getValueAsQueryToken(myContext));
+			String sourceUri = sourceParameter.getSourceUri();
+			String requestId = sourceParameter.getRequestId();
+			Predicate sourceUriPredicate = myBuilder.equal(join.get("mySourceUri"), sourceUri);
+			Predicate requestIdPredicate = myBuilder.equal(join.get("myRequestId"), requestId);
+			if (isNotBlank(sourceUri) && isNotBlank(requestId)) {
+				codePredicates.add(myBuilder.and(sourceUriPredicate, requestIdPredicate));
+			} else if (isNotBlank(sourceUri)) {
+				codePredicates.add(sourceUriPredicate);
+			} else if (isNotBlank(requestId)) {
+				codePredicates.add(requestIdPredicate);
+			}
+		}
+
+		Predicate retVal = myBuilder.or(toArray(codePredicates));
+		myPredicates.add(retVal);
+		return retVal;
+	}
+
 	private Subquery<Long> createLinkSubquery(boolean theFoundChainMatch, String theChain, String theSubResourceName, List<IQueryParameterType> theOrValues, RequestDetails theRequest) {
 		Subquery<Long> subQ = myResourceTableQuery.subquery(Long.class);
 		Root<ResourceTable> subQfrom = subQ.from(ResourceTable.class);
@@ -772,8 +831,8 @@ public class SearchBuilder implements ISearchBuilder {
 		return chainValue;
 	}
 
-	private Predicate addPredicateResourceId(String theResourceName, List<List<IQueryParameterType>> theValues, RequestDetails theRequest) {
+	private void addPredicateResourceId(String theResourceName, List<List<IQueryParameterType>> theValues, RequestDetails theRequest) {
-		return addPredicateResourceId(theValues, theResourceName, null, theRequest);
+		addPredicateResourceId(theValues, theResourceName, null, theRequest);
 	}
 
 	private Predicate addPredicateResourceId(List<List<IQueryParameterType>> theValues, String theResourceName, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequest) {
@@ -792,10 +851,10 @@ public class SearchBuilder implements ISearchBuilder {
 	private Predicate createPredicateResourceId(Root<ResourceTable> theRoot, String theResourceName, List<List<IQueryParameterType>> theValues, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequest) {
 		Predicate nextPredicate = null;
 
-		Set<Long> allOrPids = null;
+		Set<ResourcePersistentId> allOrPids = null;
 
 		for (List<? extends IQueryParameterType> nextValue : theValues) {
-			Set<Long> orPids = new HashSet<>();
+			Set<ResourcePersistentId> orPids = new HashSet<>();
 			boolean haveValue = false;
 			for (IQueryParameterType next : nextValue) {
 				String value = next.getValueAsQueryToken(myContext);
@@ -807,7 +866,7 @@ public class SearchBuilder implements ISearchBuilder {
 				if (isNotBlank(value)) {
 					haveValue = true;
 					try {
-						Long pid = myIdHelperService.translateForcedIdToPid(theResourceName, valueAsId.getIdPart(), theRequest);
+						ResourcePersistentId pid = myIdHelperService.translateForcedIdToPid(theResourceName, valueAsId.getIdPart(), theRequest);
 						orPids.add(pid);
 					} catch (ResourceNotFoundException e) {
 						// This is not an error in a search, it just results in no matchesFhirResourceDaoR4InterceptorTest
@@ -838,12 +897,12 @@ public class SearchBuilder implements ISearchBuilder {
 			switch (operation) {
 				default:
 				case eq:
-					codePredicates.add(theRoot.get("myId").as(Long.class).in(allOrPids));
+					codePredicates.add(theRoot.get("myId").as(Long.class).in(ResourcePersistentId.toLongList(allOrPids)));
 					codePredicates.add(myBuilder.equal(myResourceTableRoot.get("myResourceType"), theResourceName));
 					nextPredicate = myBuilder.and(toArray(codePredicates));
 					break;
 				case ne:
-					codePredicates.add(theRoot.get("myId").as(Long.class).in(allOrPids).not());
+					codePredicates.add(theRoot.get("myId").as(Long.class).in(ResourcePersistentId.toLongList(allOrPids)).not());
 					codePredicates.add(myBuilder.equal(myResourceTableRoot.get("myResourceType"), theResourceName));
 					nextPredicate = myBuilder.and(toArray(codePredicates));
 					break;
@@ -855,41 +914,10 @@ public class SearchBuilder implements ISearchBuilder {
 	}
 
 
-	private Predicate addPredicateSource(List<? extends IQueryParameterType> theList, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequest) {
+	private void addPredicateString(String theResourceName,
-		if (myDaoConfig.getStoreMetaSourceInformation() == DaoConfig.StoreMetaSourceInformationEnum.NONE) {
-			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "sourceParamDisabled");
-			throw new InvalidRequestException(msg);
-		}
-
-		Join<ResourceTable, ResourceHistoryProvenanceEntity> join = myResourceTableRoot.join("myProvenance", JoinType.LEFT);
-
-		List<Predicate> codePredicates = new ArrayList<>();
-
-		for (IQueryParameterType nextParameter : theList) {
-			SourceParam sourceParameter = new SourceParam(nextParameter.getValueAsQueryToken(myContext));
-			String sourceUri = sourceParameter.getSourceUri();
-			String requestId = sourceParameter.getRequestId();
-			Predicate sourceUriPredicate = myBuilder.equal(join.get("mySourceUri"), sourceUri);
-			Predicate requestIdPredicate = myBuilder.equal(join.get("myRequestId"), requestId);
-			if (isNotBlank(sourceUri) && isNotBlank(requestId)) {
-				codePredicates.add(myBuilder.and(sourceUriPredicate, requestIdPredicate));
-			} else if (isNotBlank(sourceUri)) {
-				codePredicates.add(sourceUriPredicate);
-			} else if (isNotBlank(requestId)) {
-				codePredicates.add(requestIdPredicate);
-			}
-		}
-
-		Predicate retVal = myBuilder.or(toArray(codePredicates));
-		myPredicates.add(retVal);
-		return retVal;
-	}
-
-
-	private Predicate addPredicateString(String theResourceName,
 													 String theParamName,
 													 List<? extends IQueryParameterType> theList) {
-		return addPredicateString(theResourceName,
+		addPredicateString(theResourceName,
 			theParamName,
 			theList,
 			SearchFilterParser.CompareOperation.sw);
@@ -2015,7 +2043,7 @@ public class SearchBuilder implements ISearchBuilder {
 	 * @param thePidSet May be null
 	 */
 	@Override
-	public void setPreviouslyAddedResourcePids(@Nullable List<Long> thePidSet) {
+	public void setPreviouslyAddedResourcePids(@Nullable List<ResourcePersistentId> thePidSet) {
 		myPidSet = new HashSet<>(thePidSet);
 	}
 
@@ -2081,12 +2109,12 @@ public class SearchBuilder implements ISearchBuilder {
 
 			if (myParams.get(IAnyResource.SP_RES_ID) != null) {
 				StringParam idParm = (StringParam) myParams.get(IAnyResource.SP_RES_ID).get(0).get(0);
-				Long pid = myIdHelperService.translateForcedIdToPid(myResourceName, idParm.getValue(), theRequest);
+				ResourcePersistentId pid = myIdHelperService.translateForcedIdToPid(myResourceName, idParm.getValue(), theRequest);
 				if (myAlsoIncludePids == null) {
 					myAlsoIncludePids = new ArrayList<>(1);
 				}
 				myAlsoIncludePids.add(pid);
-				myPredicates.add(myBuilder.equal(join.get("myTargetResourcePid").as(Long.class), pid));
+				myPredicates.add(myBuilder.equal(join.get("myTargetResourcePid").as(Long.class), pid.getIdAsLong()));
 			} else {
 				Predicate targetTypePredicate = myBuilder.equal(join.get("myTargetResourceType").as(String.class), myResourceName);
 				Predicate sourceTypePredicate = myBuilder.equal(myResourceTableRoot.get("myResourceType").as(String.class), myResourceName);
@@ -2110,7 +2138,7 @@ public class SearchBuilder implements ISearchBuilder {
 				}
 			}
 
-			List<Long> pids;
+			List<ResourcePersistentId> pids;
 			if (myParams.getEverythingMode() != null) {
 				pids = myFulltextSearchSvc.everything(myResourceName, myParams, theRequest);
 			} else {
@@ -2118,10 +2146,10 @@ public class SearchBuilder implements ISearchBuilder {
 			}
 			if (pids.isEmpty()) {
 				// Will never match
-				pids = Collections.singletonList(-1L);
+				pids = Collections.singletonList(new ResourcePersistentId(-1L));
 			}
 
-			myPredicates.add(myResourceTableRoot.get("myId").as(Long.class).in(pids));
+			myPredicates.add(myResourceTableRoot.get("myId").as(Long.class).in(ResourcePersistentId.toLongList(pids)));
 		}
 
 		/*
@@ -2315,21 +2343,21 @@ public class SearchBuilder implements ISearchBuilder {
 		return retVal;
 	}
 
-	private void doLoadPids(Collection<Long> thePids, Collection<Long> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation,
+	private void doLoadPids(Collection<ResourcePersistentId> thePids, Collection<ResourcePersistentId> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation,
-									Map<Long, Integer> thePosition, RequestDetails theRequest) {
+									Map<ResourcePersistentId, Integer> thePosition, RequestDetails theRequest) {
 
 		// -- get the resource from the searchView
-		Collection<ResourceSearchView> resourceSearchViewList = myResourceSearchViewDao.findByResourceIds(thePids);
+		Collection<ResourceSearchView> resourceSearchViewList = myResourceSearchViewDao.findByResourceIds(ResourcePersistentId.toLongList(thePids));
 
 		//-- preload all tags with tag definition if any
-		Map<Long, Collection<ResourceTag>> tagMap = getResourceTagMap(resourceSearchViewList);
+		Map<ResourcePersistentId, Collection<ResourceTag>> tagMap = getResourceTagMap(resourceSearchViewList);
 
-		Long resourceId;
+		ResourcePersistentId resourceId;
 		for (ResourceSearchView next : resourceSearchViewList) {
 
 			Class<? extends IBaseResource> resourceType = myContext.getResourceDefinition(next.getResourceType()).getImplementingClass();
 
-			resourceId = next.getId();
+			resourceId = new ResourcePersistentId(next.getId());
 
 			IBaseResource resource = myCallingDao.toResource(resourceType, next, tagMap.get(resourceId), theForHistoryOperation);
 			if (resource == null) {
@@ -2360,7 +2388,7 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 	}
 
-	private Map<Long, Collection<ResourceTag>> getResourceTagMap(Collection<ResourceSearchView> theResourceSearchViewList) {
+	private Map<ResourcePersistentId, Collection<ResourceTag>> getResourceTagMap(Collection<ResourceSearchView> theResourceSearchViewList) {
 
 		List<Long> idList = new ArrayList<>(theResourceSearchViewList.size());
 
@@ -2370,7 +2398,7 @@ public class SearchBuilder implements ISearchBuilder {
 				idList.add(resource.getId());
 		}
 
-		Map<Long, Collection<ResourceTag>> tagMap = new HashMap<>();
+		Map<ResourcePersistentId, Collection<ResourceTag>> tagMap = new HashMap<>();
 
 		//-- no tags
 		if (idList.size() == 0)
@@ -2380,11 +2408,11 @@ public class SearchBuilder implements ISearchBuilder {
 		Collection<ResourceTag> tagList = myResourceTagDao.findByResourceIds(idList);
 
 		//-- build the map, key = resourceId, value = list of ResourceTag
-		Long resourceId;
+		ResourcePersistentId resourceId;
 		Collection<ResourceTag> tagCol;
 		for (ResourceTag tag : tagList) {
 
-			resourceId = tag.getResourceId();
+			resourceId = new ResourcePersistentId(tag.getResourceId());
 			tagCol = tagMap.get(resourceId);
 			if (tagCol == null) {
 				tagCol = new ArrayList<>();
@@ -2399,7 +2427,7 @@ public class SearchBuilder implements ISearchBuilder {
 	}
 
 	@Override
-	public void loadResourcesByPid(Collection<Long> thePids, Collection<Long> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation, RequestDetails theDetails) {
+	public void loadResourcesByPid(Collection<ResourcePersistentId> thePids, Collection<ResourcePersistentId> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation, RequestDetails theDetails) {
 		if (thePids.isEmpty()) {
 			ourLog.debug("The include pids are empty");
 			// return;
@@ -2409,8 +2437,8 @@ public class SearchBuilder implements ISearchBuilder {
 		// when running asserts
 		assert new HashSet<>(thePids).size() == thePids.size() : "PID list contains duplicates: " + thePids;
 
-		Map<Long, Integer> position = new HashMap<>();
+		Map<ResourcePersistentId, Integer> position = new HashMap<>();
-		for (Long next : thePids) {
+		for (ResourcePersistentId next : thePids) {
 			position.put(next, theResourceListToPopulate.size());
 			theResourceListToPopulate.add(null);
 		}
@@ -2421,11 +2449,11 @@ public class SearchBuilder implements ISearchBuilder {
 		 * if it's lots of IDs. I suppose maybe we should be doing this as a join anyhow
 		 * but this should work too. Sigh.
 		 */
-		List<Long> pids = new ArrayList<>(thePids);
+		List<ResourcePersistentId> pids = new ArrayList<>(thePids);
 		for (int i = 0; i < pids.size(); i += MAXIMUM_PAGE_SIZE) {
 			int to = i + MAXIMUM_PAGE_SIZE;
 			to = Math.min(to, pids.size());
-			List<Long> pidsSubList = pids.subList(i, to);
+			List<ResourcePersistentId> pidsSubList = pids.subList(i, to);
 			doLoadPids(pidsSubList, theIncludedPids, theResourceListToPopulate, theForHistoryOperation, position, theDetails);
 		}
 
@@ -2436,7 +2464,7 @@ public class SearchBuilder implements ISearchBuilder {
 	 * so it can't be Collections.emptySet() or some such thing
 	 */
 	@Override
-	public HashSet<Long> loadIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes,
+	public HashSet<ResourcePersistentId> loadIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<ResourcePersistentId> theMatches, Set<Include> theRevIncludes,
 												 boolean theReverseMode, DateRangeParam theLastUpdated, String theSearchIdOrDescription, RequestDetails theRequest) {
 		if (theMatches.size() == 0) {
 			return new HashSet<>();
@@ -2446,9 +2474,9 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 		String searchFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
 
-		Collection<Long> nextRoundMatches = theMatches;
+		Collection<ResourcePersistentId> nextRoundMatches = theMatches;
-		HashSet<Long> allAdded = new HashSet<>();
+		HashSet<ResourcePersistentId> allAdded = new HashSet<>();
-		HashSet<Long> original = new HashSet<>(theMatches);
+		HashSet<ResourcePersistentId> original = new HashSet<>(theMatches);
 		ArrayList<Include> includes = new ArrayList<>(theRevIncludes);
 
 		int roundCounts = 0;
@@ -2458,7 +2486,7 @@ public class SearchBuilder implements ISearchBuilder {
 		do {
 			roundCounts++;
 
-			HashSet<Long> pidsToInclude = new HashSet<>();
+			HashSet<ResourcePersistentId> pidsToInclude = new HashSet<>();
 
 			for (Iterator<Include> iter = includes.iterator(); iter.hasNext(); ) {
 				Include nextInclude = iter.next();
@@ -2470,16 +2498,16 @@ public class SearchBuilder implements ISearchBuilder {
 				if (matchAll) {
 					String sql;
 					sql = "SELECT r FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
-					List<Collection<Long>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
+					List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
-					for (Collection<Long> nextPartition : partitions) {
+					for (Collection<ResourcePersistentId> nextPartition : partitions) {
 						TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
-						q.setParameter("target_pids", nextPartition);
+						q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
 						List<ResourceLink> results = q.getResultList();
 						for (ResourceLink resourceLink : results) {
 							if (theReverseMode) {
-								pidsToInclude.add(resourceLink.getSourceResourcePid());
+								pidsToInclude.add(new ResourcePersistentId(resourceLink.getSourceResourcePid()));
 							} else {
-								pidsToInclude.add(resourceLink.getTargetResourcePid());
+								pidsToInclude.add(new ResourcePersistentId(resourceLink.getTargetResourcePid()));
 							}
 						}
 					}
@@ -2523,11 +2551,11 @@ public class SearchBuilder implements ISearchBuilder {
 							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
 						}
 
-						List<Collection<Long>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
+						List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
-						for (Collection<Long> nextPartition : partitions) {
+						for (Collection<ResourcePersistentId> nextPartition : partitions) {
 							TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
 							q.setParameter("src_path", nextPath);
-							q.setParameter("target_pids", nextPartition);
+							q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
 							if (targetResourceType != null) {
 								q.setParameter("target_resource_type", targetResourceType);
 							} else if (haveTargetTypesDefinedByParam) {
@@ -2538,12 +2566,12 @@ public class SearchBuilder implements ISearchBuilder {
 								if (theReverseMode) {
 									Long pid = resourceLink.getSourceResourcePid();
 									if (pid != null) {
-										pidsToInclude.add(pid);
+										pidsToInclude.add(new ResourcePersistentId(pid));
 									}
 								} else {
 									Long pid = resourceLink.getTargetResourcePid();
 									if (pid != null) {
-										pidsToInclude.add(pid);
+										pidsToInclude.add(new ResourcePersistentId(pid));
 									}
 								}
 							}
@@ -2557,7 +2585,7 @@ public class SearchBuilder implements ISearchBuilder {
 					pidsToInclude = new HashSet<>(filterResourceIdsByLastUpdated(theEntityManager, theLastUpdated, pidsToInclude));
 				}
 			}
-			for (Long next : pidsToInclude) {
+			for (ResourcePersistentId next : pidsToInclude) {
 				if (original.contains(next) == false && allAdded.contains(next) == false) {
 					theMatches.add(next);
 				}
@@ -2573,7 +2601,7 @@ public class SearchBuilder implements ISearchBuilder {
 		// This can be used to remove results from the search result details before
 		// the user has a chance to know that they were in the results
 		if (allAdded.size() > 0) {
-			List<Long> includedPidList = new ArrayList<>(allAdded);
+			List<ResourcePersistentId> includedPidList = new ArrayList<>(allAdded);
 			JpaPreResourceAccessDetails accessDetails = new JpaPreResourceAccessDetails(includedPidList, () -> this);
 			HookParams params = new HookParams()
 				.add(IPreResourceAccessDetails.class, accessDetails)
@@ -2583,7 +2611,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 			for (int i = includedPidList.size() - 1; i >= 0; i--) {
 				if (accessDetails.isDontReturnResourceAtIndex(i)) {
-					Long value = includedPidList.remove(i);
+					ResourcePersistentId value = includedPidList.remove(i);
 					if (value != null) {
 						theMatches.remove(value);
 					}
@@ -2596,14 +2624,14 @@ public class SearchBuilder implements ISearchBuilder {
 		return allAdded;
 	}
 
-	private List<Collection<Long>> partition(Collection<Long> theNextRoundMatches, int theMaxLoad) {
+	private List<Collection<ResourcePersistentId>> partition(Collection<ResourcePersistentId> theNextRoundMatches, int theMaxLoad) {
 		if (theNextRoundMatches.size() <= theMaxLoad) {
 			return Collections.singletonList(theNextRoundMatches);
 		} else {
 
-			List<Collection<Long>> retVal = new ArrayList<>();
+			List<Collection<ResourcePersistentId>> retVal = new ArrayList<>();
-			Collection<Long> current = null;
+			Collection<ResourcePersistentId> current = null;
-			for (Long next : theNextRoundMatches) {
+			for (ResourcePersistentId next : theNextRoundMatches) {
 				if (current == null) {
 					current = new ArrayList<>(theMaxLoad);
 					retVal.add(current);
@@ -2834,28 +2862,28 @@ public class SearchBuilder implements ISearchBuilder {
 		return null;
 	}
 
-	private Predicate processFilter(SearchFilterParser.Filter filter,
+	private Predicate processFilter(SearchFilterParser.Filter theFilter,
 											  String theResourceName, RequestDetails theRequest) {
 
-		if (filter instanceof SearchFilterParser.FilterParameter) {
+		if (theFilter instanceof SearchFilterParser.FilterParameter) {
-			return processFilterParameter((SearchFilterParser.FilterParameter) filter,
+			return processFilterParameter((SearchFilterParser.FilterParameter) theFilter,
 				theResourceName, theRequest);
-		} else if (filter instanceof SearchFilterParser.FilterLogical) {
+		} else if (theFilter instanceof SearchFilterParser.FilterLogical) {
 			// Left side
-			Predicate leftPredicate = processFilter(((SearchFilterParser.FilterLogical) filter).getFilter1(),
+			Predicate xPredicate = processFilter(((SearchFilterParser.FilterLogical) theFilter).getFilter1(),
 				theResourceName, theRequest);
 
 			// Right side
-			Predicate rightPredicate = processFilter(((SearchFilterParser.FilterLogical) filter).getFilter2(),
+			Predicate yPredicate = processFilter(((SearchFilterParser.FilterLogical) theFilter).getFilter2(),
 				theResourceName, theRequest);
 
-			if (((SearchFilterParser.FilterLogical) filter).getOperation() == SearchFilterParser.FilterLogicalOperation.and) {
+			if (((SearchFilterParser.FilterLogical) theFilter).getOperation() == SearchFilterParser.FilterLogicalOperation.and) {
-				return myBuilder.and(leftPredicate, rightPredicate);
+				return myBuilder.and(xPredicate, yPredicate);
-			} else if (((SearchFilterParser.FilterLogical) filter).getOperation() == SearchFilterParser.FilterLogicalOperation.or) {
+			} else if (((SearchFilterParser.FilterLogical) theFilter).getOperation() == SearchFilterParser.FilterLogicalOperation.or) {
-				return myBuilder.or(leftPredicate, rightPredicate);
+				return myBuilder.or(xPredicate, yPredicate);
 			}
-		} else if (filter instanceof SearchFilterParser.FilterParameterGroup) {
+		} else if (theFilter instanceof SearchFilterParser.FilterParameterGroup) {
-			return processFilter(((SearchFilterParser.FilterParameterGroup) filter).getContained(),
+			return processFilter(((SearchFilterParser.FilterParameterGroup) theFilter).getContained(),
 				theResourceName, theRequest);
 		}
 		return null;
@@ -2867,29 +2895,30 @@ public class SearchBuilder implements ISearchBuilder {
 			return;
 		}
 
-		if (theParamName.equals(IAnyResource.SP_RES_ID)) {
+		switch (theParamName) {
-
+			case IAnyResource.SP_RES_ID:
 			addPredicateResourceId(theResourceName, theAndOrParams, theRequest);
+				break;
 
-		} else if (theParamName.equals(IAnyResource.SP_RES_LANGUAGE)) {
+			case IAnyResource.SP_RES_LANGUAGE:
-
 			addPredicateLanguage(theAndOrParams);
+				break;
 
-		} else if (theParamName.equals(Constants.PARAM_HAS)) {
+			case Constants.PARAM_HAS:
-
 			addPredicateHas(theAndOrParams, theRequest);
+				break;
 
-		} else if (theParamName.equals(Constants.PARAM_TAG) || theParamName.equals(Constants.PARAM_PROFILE) || theParamName.equals(Constants.PARAM_SECURITY)) {
+			case Constants.PARAM_TAG:
-
+			case Constants.PARAM_PROFILE:
+			case Constants.PARAM_SECURITY:
 			addPredicateTag(theAndOrParams, theParamName);
+				break;
 
-		} else if (theParamName.equals(Constants.PARAM_SOURCE)) {
+			case Constants.PARAM_SOURCE:
+				addPredicateSource(theAndOrParams, theRequest);
+				break;
 
-			for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
+			default:
-				addPredicateSource(nextAnd, SearchFilterParser.CompareOperation.eq, theRequest);
-			}
-
-		} else {
 
 			RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
 			if (nextParamDef != null) {
@@ -2975,6 +3004,7 @@ public class SearchBuilder implements ISearchBuilder {
 					throw new InvalidRequestException("Unknown search parameter " + theParamName + " for resource type " + theResourceName);
 				}
 			}
+				break;
 		}
 	}
 
@@ -3079,16 +3109,16 @@ public class SearchBuilder implements ISearchBuilder {
 
 	}
 
-	public class IncludesIterator extends BaseIterator<Long> implements Iterator<Long> {
+	public class IncludesIterator extends BaseIterator<ResourcePersistentId> implements Iterator<ResourcePersistentId> {
 
 		private final RequestDetails myRequest;
-		private Iterator<Long> myCurrentIterator;
+		private Iterator<ResourcePersistentId> myCurrentIterator;
 		private int myCurrentOffset;
-		private ArrayList<Long> myCurrentPids;
+		private ArrayList<ResourcePersistentId> myCurrentPids;
-		private Long myNext;
+		private ResourcePersistentId myNext;
 		private int myPageSize = myDaoConfig.getEverythingIncludesFetchPageSize();
 
-		IncludesIterator(Set<Long> thePidSet, RequestDetails theRequest) {
+		IncludesIterator(Set<ResourcePersistentId> thePidSet, RequestDetails theRequest) {
 			myCurrentPids = new ArrayList<>(thePidSet);
 			myCurrentIterator = EMPTY_LONG_LIST.iterator();
 			myCurrentOffset = 0;
@@ -3113,9 +3143,9 @@ public class SearchBuilder implements ISearchBuilder {
 					break;
 				}
 				myCurrentOffset = end;
-				Collection<Long> pidsToScan = myCurrentPids.subList(start, end);
+				Collection<ResourcePersistentId> pidsToScan = myCurrentPids.subList(start, end);
 				Set<Include> includes = Collections.singleton(new Include("*", true));
-				Set<Long> newPids = loadIncludes(myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated(), mySearchUuid, myRequest);
+				Set<ResourcePersistentId> newPids = loadIncludes(myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated(), mySearchUuid, myRequest);
 				myCurrentIterator = newPids.iterator();
 
 			}
@@ -3128,16 +3158,16 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 
 		@Override
-		public Long next() {
+		public ResourcePersistentId next() {
 			fetchNext();
-			Long retVal = myNext;
+			ResourcePersistentId retVal = myNext;
 			myNext = null;
 			return retVal;
 		}
 
 	}
 
-	private final class QueryIterator extends BaseIterator<Long> implements IResultIterator {
+	private final class QueryIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
 
 		private final SearchRuntimeDetails mySearchRuntimeDetails;
 		private final RequestDetails myRequest;
@@ -3145,8 +3175,8 @@ public class SearchBuilder implements ISearchBuilder {
 		private final boolean myHavePerftraceFoundIdHook;
 		private boolean myFirst = true;
 		private IncludesIterator myIncludesIterator;
-		private Long myNext;
+		private ResourcePersistentId myNext;
-		private Iterator<Long> myPreResultsIterator;
+		private Iterator<ResourcePersistentId> myPreResultsIterator;
 		private ScrollableResultsIterator<Long> myResultsIterator;
 		private SortSpec mySort;
 		private boolean myStillNeedToFetchIncludes;
@@ -3199,7 +3229,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 					if (myPreResultsIterator != null && myPreResultsIterator.hasNext()) {
 						while (myPreResultsIterator.hasNext()) {
-							Long next = myPreResultsIterator.next();
+							ResourcePersistentId next = myPreResultsIterator.next();
 							if (next != null)
 								if (myPidSet.add(next)) {
 									myNext = next;
@@ -3210,15 +3240,16 @@ public class SearchBuilder implements ISearchBuilder {
 
 					if (myNext == null) {
 						while (myResultsIterator.hasNext()) {
-							Long next = myResultsIterator.next();
+							Long nextLong = myResultsIterator.next();
 							if (myHavePerftraceFoundIdHook) {
 								HookParams params = new HookParams()
 									.add(Integer.class, System.identityHashCode(this))
-									.add(Object.class, next);
+									.add(Object.class, nextLong);
 								JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID, params);
 							}
 
-							if (next != null) {
+							if (nextLong != null) {
+                                ResourcePersistentId next = new ResourcePersistentId(nextLong);
 								if (myPidSet.add(next)) {
 									myNext = next;
 									break;
@@ -3236,7 +3267,7 @@ public class SearchBuilder implements ISearchBuilder {
 						}
 						if (myIncludesIterator != null) {
 							while (myIncludesIterator.hasNext()) {
-								Long next = myIncludesIterator.next();
+								ResourcePersistentId next = myIncludesIterator.next();
 								if (next != null)
 									if (myPidSet.add(next)) {
 										myNext = next;
@@ -3294,9 +3325,9 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 
 		@Override
-		public Long next() {
+		public ResourcePersistentId next() {
 			fetchNext();
-			Long retVal = myNext;
+			ResourcePersistentId retVal = myNext;
 			myNext = null;
 			Validate.isTrue(!NO_MORE.equals(retVal), "No more elements");
 			return retVal;
@@ -3430,7 +3461,7 @@ public class SearchBuilder implements ISearchBuilder {
 		return likeExpression.replace("%", "[%]") + "%";
 	}
 
-	private static List<Long> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<Long> thePids) {
+	private static List<ResourcePersistentId> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<ResourcePersistentId> thePids) {
 		if (thePids.isEmpty()) {
 			return Collections.emptyList();
 		}
@@ -3440,12 +3471,12 @@ public class SearchBuilder implements ISearchBuilder {
 		cq.select(from.get("myId").as(Long.class));
 
 		List<Predicate> lastUpdatedPredicates = createLastUpdatedPredicates(theLastUpdated, builder, from);
-		lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(thePids));
+		lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(ResourcePersistentId.toLongList(thePids)));
 
 		cq.where(SearchBuilder.toArray(lastUpdatedPredicates));
 		TypedQuery<Long> query = theEntityManager.createQuery(cq);
 
-		return query.getResultList();
+		return ResourcePersistentId.fromLongList(query.getResultList());
 	}
 
 

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

@@ -27,10 +27,9 @@ import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.query.Param;
 
-public interface IResourceIndexedSearchParamStringDao extends JpaRepository<ResourceIndexedSearchParamString, Long> {
+import java.util.List;
 
-	@Query("select count(*) from ResourceIndexedSearchParamString t WHERE t.myResourcePid = :resid")
+public interface IResourceIndexedSearchParamStringDao extends JpaRepository<ResourceIndexedSearchParamString, Long> {
-	int countForResourceId(@Param("resid") Long theResourcePid);
 
 	@Modifying
 	@Query("delete from ResourceIndexedSearchParamString t WHERE t.myResourcePid = :resid")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoBundleDstu3.java

@@ -32,18 +32,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 
 public class FhirResourceDaoBundleDstu3 extends BaseHapiFhirResourceDao<Bundle> {
 
-	@Override
+	// nothing
-	protected void preProcessResourceForStorage(Bundle theResource) {
-		super.preProcessResourceForStorage(theResource);
-
-		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
-		if (theResource.getType() == null || !allowedBundleTypes.contains(defaultString(theResource.getType().toCode()))) {
-			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType().toCode() : "(missing)");
-			throw new UnprocessableEntityException(message);
-		}
-
-	}
-
-
 
 }

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

@@ -20,9 +20,12 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -37,7 +40,6 @@ import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
-import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -63,6 +65,8 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	private ValidationSupportChain myValidationSupport;
 	@Autowired
 	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
+	@Autowired
+	private FhirContext myFhirContext;
 
 	public FhirResourceDaoCodeSystemDstu3() {
 		super();
@@ -70,10 +74,11 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
-		Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest );
+		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest );
 		List<IIdType> valueSetIds = new ArrayList<>();
-		for (Long next : ids) {
+		for (ResourcePersistentId next : ids) {
-			valueSetIds.add(new IdType("CodeSystem", next));
+			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);
+			valueSetIds.add(id);
 		}
 		return valueSetIds;
 	}
@@ -135,7 +140,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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 (!retVal.isUnchangedInCurrentOperation()) {
@@ -145,7 +150,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 			org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
 			addPidToResource(theEntity, cs);
 
-			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
+			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, (ResourceTable) theEntity);
 
 		}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.term.TranslationMatch;
 import ca.uhn.fhir.jpa.term.TranslationRequest;
 import ca.uhn.fhir.jpa.term.TranslationResult;
@@ -157,7 +158,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
 import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
 import ca.uhn.fhir.jpa.entity.SubscriptionTable;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.dstu3.model.Subscription;
@@ -65,12 +66,12 @@ public class FhirResourceDaoSubscriptionDstu3 extends BaseHapiFhirResourceDao<Su
 
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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) {
-			mySubscriptionTableDao.deleteAllForSubscription(theEntity);
+			mySubscriptionTableDao.deleteAllForSubscription((ResourceTable) theEntity);
 		}
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
@@ -411,7 +412,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -43,7 +43,7 @@ import java.util.List;
 public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 	@Autowired
-	private TransactionProcessor<Bundle, BundleEntryComponent> myTransactionProcessor;
+	private TransactionProcessor myTransactionProcessor;
 
 	@Override
 	@PostConstruct

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -60,7 +61,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 	@Override
 	public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, String theId, RequestDetails theRequest) {
 		ResourceTable target;
-		Long valueOf;
+		ResourcePersistentId valueOf;
 		try {
 			valueOf = myIdHelperService.translateForcedIdToPid(theTypeString, theId, theRequest);
 			ourLog.trace("Translated {}/{} to resource PID {}", theType, theId, valueOf);
@@ -76,12 +77,12 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 				newResource.setId(resName + "/" + theId);
 				IFhirResourceDao<IBaseResource> placeholderResourceDao = (IFhirResourceDao<IBaseResource>) myDaoRegistry.getResourceDao(newResource.getClass());
 				ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
-				valueOf = placeholderResourceDao.update(newResource).getEntity().getId();
+				valueOf = placeholderResourceDao.update(newResource).getEntity().getPersistentId();
 			} else {
 				throw new InvalidRequestException("Resource " + resName + "/" + theId + " not found, specified in path: " + theNextPathsUnsplit);
 			}
 		}
-		target = myEntityManager.find(ResourceTable.class, valueOf);
+		target = myEntityManager.find(ResourceTable.class, valueOf.getIdAsLong());
 		RuntimeResourceDefinition targetResourceDef = myContext.getResourceDefinition(theType);
 		if (target == null) {
 			String resName = targetResourceDef.getName();

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

@@ -20,8 +20,10 @@ package ca.uhn.fhir.jpa.dao.index;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
 import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
@@ -61,7 +63,7 @@ public class IdHelperService {
 	 * @throws ResourceNotFoundException If the ID can not be found
 	 */
 	@Nonnull
-	public Long translateForcedIdToPid(IIdType theId, RequestDetails theRequestDetails) {
+	public ResourcePersistentId translateForcedIdToPid(IIdType theId, RequestDetails theRequestDetails) {
 		return translateForcedIdToPid(theId.getResourceType(), theId.getIdPart(), theRequestDetails);
 	}
 
@@ -69,10 +71,10 @@ public class IdHelperService {
 	 * @throws ResourceNotFoundException If the ID can not be found
 	 */
 	@Nonnull
-	public Long translateForcedIdToPid(String theResourceName, String theResourceId, RequestDetails theRequestDetails) throws ResourceNotFoundException {
+	public ResourcePersistentId translateForcedIdToPid(String theResourceName, String theResourceId, RequestDetails theRequestDetails) throws ResourceNotFoundException {
 		// We only pass 1 input in so only 0..1 will come back
 		IdDt id = new IdDt(theResourceName, theResourceId);
-		List<Long> matches = translateForcedIdToPids(myDaoConfig, myInterceptorBroadcaster, theRequestDetails, myForcedIdDao, Collections.singletonList(id));
+		List<ResourcePersistentId> matches = translateForcedIdToPids(myDaoConfig, myInterceptorBroadcaster, theRequestDetails, myForcedIdDao, Collections.singletonList(id));
 		assert matches.size() <= 1;
 		if (matches.isEmpty()) {
 			throw new ResourceNotFoundException(id);
@@ -80,23 +82,23 @@ public class IdHelperService {
 		return matches.get(0);
 	}
 
-	public List<Long> translateForcedIdToPids(Collection<IIdType> theId, RequestDetails theRequestDetails) {
+	public List<ResourcePersistentId> translateForcedIdToPids(Collection<IIdType> theId, RequestDetails theRequestDetails) {
 		return IdHelperService.translateForcedIdToPids(myDaoConfig, myInterceptorBroadcaster, theRequestDetails, myForcedIdDao, theId);
 	}
 
-	private static List<Long> translateForcedIdToPids(DaoConfig theDaoConfig, IInterceptorBroadcaster theInterceptorBroadcaster, RequestDetails theRequest, IForcedIdDao theForcedIdDao, Collection<IIdType> theId) {
+	private static List<ResourcePersistentId> translateForcedIdToPids(DaoConfig theDaoConfig, IInterceptorBroadcaster theInterceptorBroadcaster, RequestDetails theRequest, IForcedIdDao theForcedIdDao, Collection<IIdType> theId) {
 		theId.forEach(id -> Validate.isTrue(id.hasIdPart()));
 
 		if (theId.isEmpty()) {
 			return Collections.emptyList();
 		}
 
-		List<Long> retVal = new ArrayList<>();
+		List<ResourcePersistentId> retVal = new ArrayList<>();
 
 		ListMultimap<String, String> typeToIds = MultimapBuilder.hashKeys().arrayListValues().build();
 		for (IIdType nextId : theId) {
 			if (theDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY && isValidPid(nextId)) {
-				retVal.add(nextId.getIdPartAsLong());
+				retVal.add(new ResourcePersistentId(nextId.getIdPartAsLong()));
 			} else {
 				if (nextId.hasResourceType()) {
 					typeToIds.put(nextId.getResourceType(), nextId.getIdPart());
@@ -119,18 +121,34 @@ public class IdHelperService {
 					.add(StorageProcessingMessage.class, msg);
 				JpaInterceptorBroadcaster.doCallHooks(theInterceptorBroadcaster, theRequest, Pointcut.JPA_PERFTRACE_WARNING, params);
 
-				retVal.addAll(theForcedIdDao.findByForcedId(nextIds));
+				theForcedIdDao
+					.findByForcedId(nextIds)
+					.stream()
+					.map(t->new ResourcePersistentId(t))
+					.forEach(t->retVal.add(t));
 
 			} else {
-				retVal.addAll(theForcedIdDao.findByTypeAndForcedId(nextResourceType, nextIds));
+
+				theForcedIdDao
+					.findByTypeAndForcedId(nextResourceType, nextIds)
+					.stream()
+					.map(t->new ResourcePersistentId(t))
+					.forEach(t->retVal.add(t));
+
 			}
 		}
 
 			return retVal;
 	}
 
-	String translatePidIdToForcedId(String theResourceType, Long theId) {
+	public IIdType translatePidIdToForcedId(FhirContext theCtx, String theResourceType, ResourcePersistentId theId) {
-		ForcedId forcedId = myForcedIdDao.findByResourcePid(theId);
+		IIdType retVal = theCtx.getVersion().newIdType();
+		retVal.setValue(translatePidIdToForcedId(theResourceType, theId));
+		return retVal;
+	}
+
+	public String translatePidIdToForcedId(String theResourceType, ResourcePersistentId theId) {
+		ForcedId forcedId = myForcedIdDao.findByResourcePid(theId.getIdAsLong());
 		if (forcedId != null) {
 			return forcedId.getResourceType() + '/' + forcedId.getForcedId();
 		} else {

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

@@ -25,9 +25,9 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.IDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
 import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
+import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
 import ca.uhn.fhir.jpa.model.entity.ResourceLink;
@@ -54,7 +54,14 @@ import org.springframework.stereotype.Service;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
@@ -238,7 +245,7 @@ public class SearchParamWithInlineReferencesExtractor {
 					throw new InvalidRequestException(msg);
 				}
 				Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
-				Set<Long> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest);
+				Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest);
 				if (matches.isEmpty()) {
 					String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
 					throw new ResourceNotFoundException(msg);
@@ -247,7 +254,7 @@ public class SearchParamWithInlineReferencesExtractor {
 					String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlMultipleMatches", nextId.getValue());
 					throw new PreconditionFailedException(msg);
 				}
-				Long next = matches.iterator().next();
+				ResourcePersistentId next = matches.iterator().next();
 				String newId = myIdHelperService.translatePidIdToForcedId(resourceTypeString, next);
 				ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
 				nextRef.setReference(newId);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoBundleR4.java

@@ -33,16 +33,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 
 public class FhirResourceDaoBundleR4 extends BaseHapiFhirResourceDao<Bundle> {
 
-	@Override
+	// nothing for now
-	protected void preProcessResourceForStorage(Bundle theResource) {
-		super.preProcessResourceForStorage(theResource);
-
-		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
-		if (theResource.getType() == null || !allowedBundleTypes.contains(defaultString(theResource.getType().toCode()))) {
-			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType().toCode() : "(missing)");
-			throw new UnprocessableEntityException(message);
-		}
-
-	}
 
 }

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

@@ -20,9 +20,12 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -39,7 +42,6 @@ import org.hl7.fhir.r4.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.IdType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -60,14 +62,17 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	private ValidationSupportChain myValidationSupport;
 	@Autowired
 	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
+	@Autowired
+	private FhirContext myFhirContext;
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
 		List<IIdType> valueSetIds;
-		Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		valueSetIds = new ArrayList<>();
-		for (Long next : ids) {
+		for (ResourcePersistentId next : ids) {
-			valueSetIds.add(new IdType("CodeSystem", next));
+			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);
+			valueSetIds.add(id);
 		}
 		return valueSetIds;
 	}
@@ -132,7 +137,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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);
 
@@ -140,7 +145,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 			CodeSystem cs = (CodeSystem) theResource;
 			addPidToResource(theEntity, theResource);
 
-			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
+			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, (ResourceTable) theEntity);
 		}
 
 		return retVal;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
@@ -157,7 +158,7 @@ public class FhirResourceDaoConceptMapR4 extends BaseHapiFhirResourceDao<Concept
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSubscriptionR4.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
 import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
 import ca.uhn.fhir.jpa.entity.SubscriptionTable;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -65,7 +66,7 @@ public class FhirResourceDaoSubscriptionR4 extends BaseHapiFhirResourceDao<Subsc
 
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
@@ -392,7 +393,7 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java

@@ -45,7 +45,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoR4.class);
 
 	@Autowired
-	private TransactionProcessor<Bundle, BundleEntryComponent> myTransactionProcessor;
+	private TransactionProcessor myTransactionProcessor;
 
 	@Override
 	@PostConstruct

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoBundleR5.java

@@ -30,16 +30,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 
 public class FhirResourceDaoBundleR5 extends BaseHapiFhirResourceDao<Bundle> {
 
-	@Override
+	// nothing
-	protected void preProcessResourceForStorage(Bundle theResource) {
-		super.preProcessResourceForStorage(theResource);
-
-		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
-		if (theResource.getType() == null || !allowedBundleTypes.contains(defaultString(theResource.getType().toCode()))) {
-			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType().toCode() : "(missing)");
-			throw new UnprocessableEntityException(message);
-		}
-
-	}
 
 }

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

@@ -20,10 +20,14 @@ package ca.uhn.fhir.jpa.dao.r5;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -39,7 +43,6 @@ import org.hl7.fhir.r5.hapi.validation.ValidationSupportChain;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Coding;
-import org.hl7.fhir.r5.model.IdType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
@@ -60,14 +63,19 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	private ValidationSupportChain myValidationSupport;
 	@Autowired
 	protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
+	@Autowired
+	protected IdHelperService myIdHelperService;
+	@Autowired
+	private FhirContext myFhirContext;
 
 	@Override
 	public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
 		List<IIdType> valueSetIds;
-		Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
+		Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
 		valueSetIds = new ArrayList<>();
-		for (Long next : ids) {
+		for (ResourcePersistentId next : ids) {
-			valueSetIds.add(new IdType("CodeSystem", next));
+			IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);
+			valueSetIds.add(id);
 		}
 		return valueSetIds;
 	}
@@ -132,7 +140,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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 (!retVal.isUnchangedInCurrentOperation()) {
@@ -140,7 +148,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 			CodeSystem cs = (CodeSystem) theResource;
 			addPidToResource(theEntity, theResource);
 
-			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
+			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), (ResourceTable) theEntity);
 		}
 
 		return retVal;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
 import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.TranslationMatch;
@@ -158,8 +159,8 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
-													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
+												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 		if (!retVal.isUnchangedInCurrentOperation()) {
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSubscriptionR5.java

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
 import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
 import ca.uhn.fhir.jpa.entity.SubscriptionTable;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -74,7 +75,7 @@ public class FhirResourceDaoSubscriptionR5 extends BaseHapiFhirResourceDao<Subsc
 
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
+	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource 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);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.LogicUtil;
@@ -404,7 +405,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
 	}
 
 	@Override
-	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirSystemDaoR5.java

@@ -45,7 +45,7 @@ public class FhirSystemDaoR5 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoR5.class);
 
 	@Autowired
-	private TransactionProcessor<Bundle, BundleEntryComponent> myTransactionProcessor;
+	private TransactionProcessor myTransactionProcessor;
 
 	@Override
 	@PostConstruct

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictService.java

@@ -132,12 +132,12 @@ public class DeleteConflictService {
 		}
 	}
 
-	public void validateDeleteConflictsEmptyOrThrowException(DeleteConflictList theDeleteConflicts) {
+	public static void validateDeleteConflictsEmptyOrThrowException(FhirContext theFhirContext, DeleteConflictList theDeleteConflicts) {
 		if (theDeleteConflicts.isEmpty()) {
 			return;
 		}
 
-		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(myFhirContext);
+		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(theFhirContext);
 		String firstMsg = null;
 
 		Iterator<DeleteConflict> iterator = theDeleteConflicts.iterator();
@@ -154,7 +154,7 @@ public class DeleteConflictService {
 			if (firstMsg == null) {
 				firstMsg = msg;
 			}
-			OperationOutcomeUtil.addIssue(myFhirContext, oo, BaseHapiFhirDao.OO_SEVERITY_ERROR, msg, null, "processing");
+			OperationOutcomeUtil.addIssue(theFhirContext, oo, BaseHapiFhirDao.OO_SEVERITY_ERROR, msg, null, "processing");
 		}
 
 		throw new ResourceVersionConflictException(firstMsg, oo);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/JpaStorageServices.java

@@ -42,6 +42,7 @@ import org.hl7.fhir.utilities.graphql.Value;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
+import javax.annotation.Nullable;
 import java.util.List;
 
 public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implements IGraphQLStorageServices {
@@ -145,4 +146,10 @@ public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implement
 	public IBaseBundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
 		throw new NotImplementedOperationException("Not yet able to handle this GraphQL request");
 	}
+
+	@Nullable
+	@Override
+	protected String getResourceName() {
+		return null;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/JpaPreResourceAccessDetails.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.interceptor;
  */
 
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
 import ca.uhn.fhir.util.ICallable;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -36,12 +37,12 @@ import java.util.List;
 @NotThreadSafe
 public class JpaPreResourceAccessDetails implements IPreResourceAccessDetails {
 
-	private final List<Long> myResourcePids;
+	private final List<ResourcePersistentId> myResourcePids;
 	private final boolean[] myBlocked;
 	private final ICallable<ISearchBuilder> mySearchBuilderSupplier;
 	private List<IBaseResource> myResources;
 
-	public JpaPreResourceAccessDetails(List<Long> theResourcePids, ICallable<ISearchBuilder> theSearchBuilderSupplier) {
+	public JpaPreResourceAccessDetails(List<ResourcePersistentId> theResourcePids, ICallable<ISearchBuilder> theSearchBuilderSupplier) {
 		myResourcePids = theResourcePids;
 		myBlocked = new boolean[myResourcePids.size()];
 		mySearchBuilderSupplier = theSearchBuilderSupplier;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/ISearchCoordinatorSvc.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.search;
  */
 
 import ca.uhn.fhir.jpa.dao.IDao;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -34,7 +35,7 @@ public interface ISearchCoordinatorSvc {
 
 	void cancelAllActiveSearches();
 
-	List<Long> getResources(String theUuid, int theFrom, int theTo, @Nullable RequestDetails theRequestDetails);
+	List<ResourcePersistentId> getResources(String theUuid, int theFrom, int theTo, @Nullable RequestDetails theRequestDetails);
 
 	IBundleProvider registerSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, CacheControlDirective theCacheControlDirective, @Nullable RequestDetails theRequestDetails);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java

@@ -26,6 +26,7 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.dao.IDao;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
@@ -175,7 +176,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		Class<? extends IBaseResource> resourceType = myContext.getResourceDefinition(resourceName).getImplementingClass();
 		sb.setType(resourceType, resourceName);
 
-		final List<Long> pidsSubList = mySearchCoordinatorSvc.getResources(myUuid, theFromIndex, theToIndex, myRequest);
+		final List<ResourcePersistentId> pidsSubList = mySearchCoordinatorSvc.getResources(myUuid, theFromIndex, theToIndex, myRequest);
 
 		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
 		template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
@@ -310,15 +311,15 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 
 	// Note: Leave as protected, HSPC depends on this
 	@SuppressWarnings("WeakerAccess")
-	protected List<IBaseResource> toResourceList(ISearchBuilder theSearchBuilder, List<Long> thePids) {
+	protected List<IBaseResource> toResourceList(ISearchBuilder theSearchBuilder, List<ResourcePersistentId> thePids) {
-		Set<Long> includedPids = new HashSet<>();
+		Set<ResourcePersistentId> includedPids = new HashSet<>();
 
 		if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
 			includedPids.addAll(theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated(), myUuid, myRequest));
 			includedPids.addAll(theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated(), myUuid, myRequest));
 		}
 
-		List<Long> includedPidList = new ArrayList<>(includedPids);
+		List<ResourcePersistentId> includedPidList = new ArrayList<>(includedPids);
 
 		// Execute the query and make sure we return distinct results
 		List<IBaseResource> resources = new ArrayList<>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaSearchFirstPageBundleProvider.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.search;
 
 import ca.uhn.fhir.jpa.dao.IDao;
 import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl.SearchTask;
@@ -66,7 +67,7 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
 		mySearchTask.awaitInitialSync();
 
 		ourLog.trace("Fetching search resource PIDs from task: {}", mySearchTask.getClass());
-		final List<Long> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
+		final List<ResourcePersistentId> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
 		ourLog.trace("Done fetching search resource PIDs");
 
 		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchInclude;
 import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
@@ -173,7 +174,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	 */
 	@Override
 	@Transactional(propagation = Propagation.NEVER)
-	public List<Long> getResources(final String theUuid, int theFrom, int theTo, @Nullable RequestDetails theRequestDetails) {
+	public List<ResourcePersistentId> getResources(final String theUuid, int theFrom, int theTo, @Nullable RequestDetails theRequestDetails) {
 		TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
 
@@ -193,7 +194,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			if (myNeverUseLocalSearchForUnitTests == false) {
 				if (searchTask != null) {
 					ourLog.trace("Local search found");
-					List<Long> resourcePids = searchTask.getResourcePids(theFrom, theTo);
+					List<ResourcePersistentId> resourcePids = searchTask.getResourcePids(theFrom, theTo);
 					ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
 
 					/*
@@ -249,7 +250,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 		ourLog.trace("Finished looping");
 
-		List<Long> pids = mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
+		List<ResourcePersistentId> pids = mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
 		if (pids == null) {
 			throw newResourceGoneException(theUuid);
 		}
@@ -446,7 +447,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		return txTemplate.execute(t -> {
 
 			// Load the results synchronously
-			final List<Long> pids = new ArrayList<>();
+			final List<ResourcePersistentId> pids = new ArrayList<>();
 
 			try (IResultIterator resultIter = theSb.createQuery(theParams, searchRuntimeDetails, theRequestDetails)) {
 				while (resultIter.hasNext()) {
@@ -485,10 +486,10 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			 * On the other hand for async queries we load includes/revincludes
 			 * individually for pages as we return them to clients
 			 */
-			final Set<Long> includedPids = new HashSet<>();
+			final Set<ResourcePersistentId> includedPids = new HashSet<>();
 			includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
 			includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
-			List<Long> includedPidsList = new ArrayList<>(includedPids);
+			List<ResourcePersistentId> includedPidsList = new ArrayList<>(includedPids);
 
 			List<IBaseResource> resources = new ArrayList<>();
 			theSb.loadResourcesByPid(pids, includedPidsList, resources, false, theRequestDetails);
@@ -580,10 +581,10 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		private final SearchParameterMap myParams;
 		private final IDao myCallingDao;
 		private final String myResourceType;
-		private final ArrayList<Long> mySyncedPids = new ArrayList<>();
+		private final ArrayList<ResourcePersistentId> mySyncedPids = new ArrayList<>();
 		private final CountDownLatch myInitialCollectionLatch = new CountDownLatch(1);
 		private final CountDownLatch myCompletionLatch;
-		private final ArrayList<Long> myUnsyncedPids = new ArrayList<>();
+		private final ArrayList<ResourcePersistentId> myUnsyncedPids = new ArrayList<>();
 		private final RequestDetails myRequest;
 		private Search mySearch;
 		private boolean myAbortRequested;
@@ -591,7 +592,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		private int myCountSavedThisPass = 0;
 		private int myCountBlockedThisPass = 0;
 		private boolean myAdditionalPrefetchThresholdsRemaining;
-		private List<Long> myPreviouslyAddedResourcePids;
+		private List<ResourcePersistentId> myPreviouslyAddedResourcePids;
 		private Integer myMaxResultsToFetch;
 		private SearchRuntimeDetails mySearchRuntimeDetails;
 
@@ -635,7 +636,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			return myInitialCollectionLatch;
 		}
 
-		void setPreviouslyAddedResourcePids(List<Long> thePreviouslyAddedResourcePids) {
+		void setPreviouslyAddedResourcePids(List<ResourcePersistentId> thePreviouslyAddedResourcePids) {
 			myPreviouslyAddedResourcePids = thePreviouslyAddedResourcePids;
 			myCountSavedTotal = myPreviouslyAddedResourcePids.size();
 		}
@@ -649,7 +650,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		}
 
 		@Nonnull
-		List<Long> getResourcePids(int theFromIndex, int theToIndex) {
+		List<ResourcePersistentId> getResourcePids(int theFromIndex, int theToIndex) {
 			ourLog.debug("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
 
 			boolean keepWaiting;
@@ -673,6 +674,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 								break;
 							case FAILED:
 							case FINISHED:
+							case GONE:
 							default:
 								keepWaiting = false;
 								break;
@@ -690,7 +692,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 			ourLog.debug("Proceeding, as we have {} results", mySyncedPids.size());
 
-			ArrayList<Long> retVal = new ArrayList<>();
+			ArrayList<ResourcePersistentId> retVal = new ArrayList<>();
 			synchronized (mySyncedPids) {
 				verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
 
@@ -713,7 +715,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 			txTemplate.execute(new TransactionCallbackWithoutResult() {
 				@Override
-				protected void doInTransactionWithoutResult(@NotNull TransactionStatus theArg0) {
+				protected void doInTransactionWithoutResult(@Nonnull @NotNull TransactionStatus theArg0) {
 					doSaveSearch();
 				}
 
@@ -725,12 +727,12 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
 			txTemplate.execute(new TransactionCallbackWithoutResult() {
 				@Override
-				protected void doInTransactionWithoutResult(@NotNull TransactionStatus theArg0) {
+				protected void doInTransactionWithoutResult(@Nonnull @NotNull TransactionStatus theArg0) {
 					if (mySearch.getId() == null) {
 						doSaveSearch();
 					}
 
-					ArrayList<Long> unsyncedPids = myUnsyncedPids;
+					ArrayList<ResourcePersistentId> unsyncedPids = myUnsyncedPids;
 					int countBlocked = 0;
 
 					// Interceptor call: STORAGE_PREACCESS_RESOURCES
@@ -847,7 +849,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 				txTemplate.execute(new TransactionCallbackWithoutResult() {
 					@Override
-					protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+					protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theStatus) {
 						doSearch();
 					}
 				});
@@ -962,7 +964,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
 				txTemplate.execute(new TransactionCallbackWithoutResult() {
 					@Override
-					protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+					protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theArg0) {
 						mySearch.setTotalCount(count.intValue());
 						if (wantOnlyCount) {
 							mySearch.setStatus(SearchStatusEnum.FINISHED);
@@ -1093,7 +1095,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
 				txTemplate.afterPropertiesSet();
 				txTemplate.execute(t -> {
-					List<Long> previouslyAddedResourcePids = mySearchResultCacheSvc.fetchAllResultPids(getSearch());
+					List<ResourcePersistentId> previouslyAddedResourcePids = mySearchResultCacheSvc.fetchAllResultPids(getSearch());
 					if (previouslyAddedResourcePids == null) {
 						throw newResourceGoneException(getSearch().getUuid());
 					}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchResultCacheSvcImpl.java

@@ -20,19 +20,17 @@ package ca.uhn.fhir.jpa.search.cache;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchResult;
-import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Lists;
-import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Pageable;
 
 import javax.transaction.Transactional;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
@@ -46,7 +44,7 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 
 	@Override
 	@Transactional(Transactional.TxType.REQUIRED)
-	public List<Long> fetchResultPids(Search theSearch, int theFrom, int theTo) {
+	public List<ResourcePersistentId> fetchResultPids(Search theSearch, int theFrom, int theTo) {
 		final Pageable page = toPage(theFrom, theTo);
 		if (page == null) {
 			return Collections.emptyList();
@@ -58,28 +56,28 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 
 		ourLog.debug("fetchResultPids for range {}-{} returned {} pids", theFrom, theTo, retVal.size());
 
-		return new ArrayList<>(retVal);
+		return ResourcePersistentId.fromLongList(retVal);
 	}
 
 	@Override
 	@Transactional(Transactional.TxType.REQUIRED)
-	public List<Long> fetchAllResultPids(Search theSearch) {
+	public List<ResourcePersistentId> fetchAllResultPids(Search theSearch) {
 		List<Long> retVal = mySearchResultDao.findWithSearchPidOrderIndependent(theSearch.getId());
 		ourLog.trace("fetchAllResultPids returned {} pids", retVal.size());
-		return retVal;
+		return ResourcePersistentId.fromLongList(retVal);
 	}
 
 	@Override
 	@Transactional(Transactional.TxType.REQUIRED)
-	public void storeResults(Search theSearch, List<Long> thePreviouslyStoredResourcePids, List<Long> theNewResourcePids) {
+	public void storeResults(Search theSearch, List<ResourcePersistentId> thePreviouslyStoredResourcePids, List<ResourcePersistentId> theNewResourcePids) {
 		List<SearchResult> resultsToSave = Lists.newArrayList();
 
 		ourLog.trace("Storing {} results with {} previous for search", theNewResourcePids.size(), thePreviouslyStoredResourcePids.size());
 
 		int order = thePreviouslyStoredResourcePids.size();
-		for (Long nextPid : theNewResourcePids) {
+		for (ResourcePersistentId nextPid : theNewResourcePids) {
 			SearchResult nextResult = new SearchResult(theSearch);
-			nextResult.setResourcePid(nextPid);
+			nextResult.setResourcePid(nextPid.getIdAsLong());
 			nextResult.setOrder(order);
 			resultsToSave.add(nextResult);
 			ourLog.trace("Saving ORDER[{}] Resource {}", order, nextResult.getResourcePid());
@@ -90,10 +88,4 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 		mySearchResultDao.saveAll(resultsToSave);
 	}
 
-	@VisibleForTesting
-	void setSearchDaoResultForUnitTest(ISearchResultDao theSearchResultDao) {
-		mySearchResultDao = theSearchResultDao;
-	}
-
-
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/ISearchResultCacheSvc.java

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.search.cache;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.entity.Search;
 
 import javax.annotation.Nullable;
@@ -31,7 +32,7 @@ public interface ISearchResultCacheSvc {
 	 * @param thePreviouslyStoredResourcePids A list of resource PIDs that have previously been saved to this search
 	 * @param theNewResourcePids              A list of new resoure PIDs to add to this search (these ones have not been previously saved)
 	 */
-	void storeResults(Search theSearch, List<Long> thePreviouslyStoredResourcePids, List<Long> theNewResourcePids);
+	void storeResults(Search theSearch, List<ResourcePersistentId> thePreviouslyStoredResourcePids, List<ResourcePersistentId> theNewResourcePids);
 
 	/**
 	 * Fetch a sunset of the search result IDs from the cache
@@ -43,7 +44,7 @@ public interface ISearchResultCacheSvc {
 	 * have been removed from the cache for some reason, such as expiry or manual purge)
 	 */
 	@Nullable
-	List<Long> fetchResultPids(Search theSearch, int theFrom, int theTo);
+	List<ResourcePersistentId> fetchResultPids(Search theSearch, int theFrom, int theTo);
 
 	/**
 	 * Fetch all result PIDs for a given search with no particular order required
@@ -53,6 +54,6 @@ public interface ISearchResultCacheSvc {
 	 * have been removed from the cache for some reason, such as expiry or manual purge)
 	 */
 	@Nullable
-	List<Long> fetchAllResultPids(Search theSearch);
+	List<ResourcePersistentId> fetchAllResultPids(Search theSearch);
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionTriggeringSvcImpl.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
 import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
@@ -37,8 +38,6 @@ import ca.uhn.fhir.model.dstu2.valueset.ResourceTypeEnum;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@@ -252,12 +251,12 @@ public class SubscriptionTriggeringSvcImpl implements ISubscriptionTriggeringSvc
 				toIndex = Math.min(toIndex, theJobDetails.getCurrentSearchCount());
 			}
 			ourLog.info("Triggering job[{}] search {} requesting resources {} - {}", theJobDetails.getJobId(), theJobDetails.getCurrentSearchUuid(), fromIndex, toIndex);
-			List<Long> resourceIds = mySearchCoordinatorSvc.getResources(theJobDetails.getCurrentSearchUuid(), fromIndex, toIndex, null);
+			List<ResourcePersistentId> resourceIds = mySearchCoordinatorSvc.getResources(theJobDetails.getCurrentSearchUuid(), fromIndex, toIndex, null);
 
 			ourLog.info("Triggering job[{}] delivering {} resources", theJobDetails.getJobId(), resourceIds.size());
 			int highestIndexSubmitted = theJobDetails.getCurrentSearchLastUploadedIndex();
 
-			for (Long next : resourceIds) {
+			for (ResourcePersistentId next : resourceIds) {
 				IBaseResource nextResource = resourceDao.readByPid(next);
 				Future<Void> future = submitResource(theJobDetails.getSubscriptionId(), nextResource);
 				futures.add(Pair.of(nextResource.getIdElement().getIdPart(), future));

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

@@ -33,6 +33,7 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
@@ -338,8 +339,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 		Optional<TermValueSet> optionalTermValueSet;
 		if (theValueSetToExpand.hasId()) {
-			Long valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSetToExpand.getIdElement());
+			ResourcePersistentId valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSetToExpand.getIdElement());
-			optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
+			optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
 		} else if (theValueSetToExpand.hasUrl()) {
 			optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
 		} else {
@@ -1113,8 +1114,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 	@Override
 	public boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet) {
-		Long valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSet.getIdElement());
+		ResourcePersistentId valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSet.getIdElement());
-		Optional<TermValueSet> optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
+		Optional<TermValueSet> optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
 
 		if (!optionalTermValueSet.isPresent()) {
 			ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory code validation. {}", getValueSetInfo(theValueSet));
@@ -1136,14 +1137,14 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
 
 		ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
-		Long valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSet.getIdElement());
+		ResourcePersistentId valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSet.getIdElement());
 
 		List<TermValueSetConcept> concepts = new ArrayList<>();
 		if (isNotBlank(theCode)) {
-			if (isNotBlank(theSystem)) {
+			if (Constants.codeSystemNotNeeded(theSystem)) {
+				concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid.getIdAsLong(), theCode));
+			} else if (isNotBlank(theSystem)) {
 				concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theSystem, theCode));
-			} if (Constants.codeSystemNotNeeded(theSystem)) {
-				concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid, theCode));
 			}
 		} else if (theCoding != null) {
 			if (theCoding.hasSystem() && theCoding.hasCode()) {
@@ -1173,9 +1174,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		return null;
 	}
 
-	private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(Long theResourcePid, String theSystem, String theCode) {
+	private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(ResourcePersistentId theResourcePid, String theSystem, String theCode) {
 		List<TermValueSetConcept> retVal = new ArrayList<>();
-		Optional<TermValueSetConcept> optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(theResourcePid, theSystem, theCode);
+		Optional<TermValueSetConcept> optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(theResourcePid.getIdAsLong(), theSystem, theCode);
 		optionalTermValueSetConcept.ifPresent(retVal::add);
 		return retVal;
 	}

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

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.entity.*;
@@ -114,11 +115,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 	private IResourceTableDao myResourceTableDao;
 
 	@Override
-	public Long getValueSetResourcePid(IIdType theIdType) {
+	public ResourcePersistentId getValueSetResourcePid(IIdType theIdType) {
 		return getValueSetResourcePid(theIdType, null);
 	}
 
-	private Long getValueSetResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
+	private ResourcePersistentId getValueSetResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
 		return myIdHelperService.translateForcedIdToPid(theIdType, theRequestDetails);
 	}
 
@@ -315,7 +316,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE || theCodeSystem.getContent() == null || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
 				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
 
-				Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
+				ResourcePersistentId codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
 
 				/*
 				 * If this is a not-present codesystem, we don't want to store a new version if one
@@ -349,8 +350,8 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
 
 		IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource);
-		Long codeSystemResourcePid = myIdHelperService.translateForcedIdToPid(csId, theRequest);
+		ResourcePersistentId codeSystemResourcePid = myIdHelperService.translateForcedIdToPid(csId, theRequest);
-		ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid);
+		ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid.getIdAsLong());
 
 		ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
 
@@ -366,14 +367,14 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
-	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
+	public void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
 		ourLog.debug("Storing code system");
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
 
 		// Grab the existing versions so we can delete them later
-		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid);
+		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid.getIdAsLong());
 
 		/*
 		 * For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
@@ -598,11 +599,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 
 	}
 
-	private Long getCodeSystemResourcePid(IIdType theIdType) {
+	private ResourcePersistentId getCodeSystemResourcePid(IIdType theIdType) {
 		return getCodeSystemResourcePid(theIdType, null);
 	}
 
-	private Long getCodeSystemResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
+	private ResourcePersistentId getCodeSystemResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
 		return myIdHelperService.translateForcedIdToPid(theIdType, theRequestDetails);
 	}
 
@@ -676,10 +677,10 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 	}
 
 	@Nonnull
-	private TermCodeSystem getOrCreateTermCodeSystem(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
+	private TermCodeSystem getOrCreateTermCodeSystem(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
 		TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
 		if (codeSystem == null) {
-			codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid);
+			codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid.getIdAsLong());
 			if (codeSystem == null) {
 				codeSystem = new TermCodeSystem();
 			}

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.term.api;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
@@ -40,7 +41,7 @@ public interface ITermCodeSystemStorageSvc {
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 
-	void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
+	void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
 
 	/**
 	 * @return Returns the ID of the created/updated code system
@@ -55,5 +56,5 @@ public interface ITermCodeSystemStorageSvc {
 
 	int saveConcept(TermConcept theNextConcept);
 
-	Long getValueSetResourcePid(IIdType theIdElement);
+	ResourcePersistentId getValueSetResourcePid(IIdType theIdElement);
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java

@@ -24,7 +24,7 @@ import java.sql.SQLException;
 import java.util.Properties;
 import java.util.concurrent.TimeUnit;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.fail;
 
 @Configuration
 @Import(TestJPAConfig.class)

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
@@ -1537,7 +1538,7 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		String methodName = "testSearchValueQuantity";
 
 		QuantityParam param;
-		Set<Long> found;
+		Set<ResourcePersistentId> found;
 		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
 		found = myObservationDao.searchForIds(new SearchParameterMap("value-quantity", param), null);
 		int initialSize = found.size();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -3,7 +3,7 @@ package ca.uhn.fhir.jpa.dao.dstu2;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.JpaResourceDao;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3Test;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
@@ -221,8 +221,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			assertThat(toUnqualifiedVersionlessIdValues(found), hasItem(id2.getValue()));
 		}
 		{
-			Set<Long> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
+			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
-			assertThat(found, not(hasItem(id2.getIdPartAsLong())));
+			assertThat(ResourcePersistentId.toLongList(found), not(hasItem(id2.getIdPartAsLong())));
 		}
 	}
 
@@ -1548,7 +1548,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 				"}\n";
 		//@formatter:on
 
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		Organization org = myFhirCtx.newJsonParser().parseResource(Organization.class, inputStr);
@@ -2677,7 +2677,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 		assertThat(str.length(), greaterThan(ResourceIndexedSearchParamString.MAX_LENGTH));
 
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -2825,7 +2825,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 		String subStr1 = longStr1.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
 		String subStr2 = longStr2.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new IdentifierDt(subStr1, subStr2)), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new IdentifierDt(subStr1, subStr2)), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2UpdateTest.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
@@ -166,9 +167,9 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
 		p2.addName().addFamily("Tester").addGiven("testUpdateMaintainsSearchParamsDstu2BBB");
 		myPatientDao.create(p2, mySrd);
 
-		Set<Long> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsDstu2AAA")), null);
+		Set<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsDstu2AAA")), null);
 		assertEquals(1, ids.size());
-		assertThat(ids, contains(p1id.getIdPartAsLong()));
+		assertThat(ResourcePersistentId.toLongList(ids), contains(p1id.getIdPartAsLong()));
 
 		// Update the name
 		p1.getNameFirstRep().getGivenFirstRep().setValue("testUpdateMaintainsSearchParamsDstu2BBB");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSearchDaoDstu2Test.java

@@ -6,6 +6,7 @@ import static org.junit.Assert.assertThat;
 
 import java.util.List;
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import org.junit.AfterClass;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -65,8 +66,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// OR
 		{
@@ -74,8 +75,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}		
 		// AND
 		{
@@ -84,8 +85,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// AND OR
 		{
@@ -94,8 +95,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}
 		// All Resource Types
 		{
@@ -103,8 +104,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")).addOr(new StringParam("DDD")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(null, map);
+			List<ResourcePersistentId> found = mySearchDao.search(null, map);
-			assertThat(found, containsInAnyOrder(id1, id2, id3));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2, id3));
 		}
 
 	}
@@ -133,8 +134,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// OR
 		{
@@ -142,8 +143,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}		
 		// AND
 		{
@@ -152,8 +153,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// AND OR
 		{
@@ -162,8 +163,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}
 		// Tag Contents
 		{
@@ -171,8 +172,8 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("div")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, empty());
+			assertThat(ResourcePersistentId.toLongList(found), empty());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
@@ -101,7 +102,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
 		parentC.addChild(childCA, RelationshipTypeEnum.ISA);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		return codeSystem;
 	}
 
@@ -132,7 +133,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 			parentB.addChild(childI, RelationshipTypeEnum.ISA);
 		}
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
 	}
 
 	private void createExternalCsAndLocalVs() {
@@ -167,7 +168,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
 		dogs.addChild(beagle, RelationshipTypeEnum.ISA);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM,"SYSTEM NAME", "SYSTEM VERSION" , cs, table);
 		return codeSystem;
 	}
 
@@ -686,7 +687,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		cs.setResource(table);
 		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
 		cs.getConcepts().add(parentA);
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs, table);
 
 		StringType code = new StringType("ParentA");
 		StringType system = new StringType("http://snomed.info/sct");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
@@ -43,6 +44,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
@@ -214,12 +216,12 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		IIdType id2 = myObservationDao.create(o2, mySrd).getId();
 
 		{
-			Set<Long> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
+			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
-			assertThat(found, hasItem(id2.getIdPartAsLong()));
+			assertThat(ResourcePersistentId.toLongList(found), hasItem(id2.getIdPartAsLong()));
 		}
 		{
-			Set<Long> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
+			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
-			assertThat(found, not(hasItem(id2.getIdPartAsLong())));
+			assertThat(ResourcePersistentId.toLongList(found), not(hasItem(id2.getIdPartAsLong())));
 		}
 	}
 
@@ -421,7 +423,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		String name = "profiles-resources";
 		ourLog.info("Uploading " + name);
 		String vsContents;
-		vsContents = IOUtils.toString(FhirResourceDaoDstu3Test.class.getResourceAsStream("/org/hl7/fhir/dstu3/model/profile/" + name + ".xml"), "UTF-8");
+		vsContents = IOUtils.toString(FhirResourceDaoDstu3Test.class.getResourceAsStream("/org/hl7/fhir/dstu3/model/profile/" + name + ".xml"), StandardCharsets.UTF_8);
 
 		bundle = myFhirCtx.newXmlParser().parseResource(org.hl7.fhir.dstu3.model.Bundle.class, vsContents);
 		for (BundleEntryComponent i : bundle.getEntry()) {
@@ -603,13 +605,13 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		 * be fixed.
 		 */
 		assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirDao.OO_SEVERITY_ERROR);
-		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
+		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirDao.OO_SEVERITY_ERROR);
 		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirDao.OO_SEVERITY_ERROR);
 		assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirDao.OO_SEVERITY_INFO);
-		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_INFO);
+		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirDao.OO_SEVERITY_INFO);
 		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirDao.OO_SEVERITY_INFO);
 		assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirDao.OO_SEVERITY_WARN);
-		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_WARN);
+		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirDao.OO_SEVERITY_WARN);
 		assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirDao.OO_SEVERITY_WARN);
 	}
 
@@ -985,7 +987,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	@Test
 	public void testDeleteResource() {
-		int initialHistory = myPatientDao.history((Date) null, null, mySrd).size();
+		int initialHistory = myPatientDao.history(null, null, mySrd).size();
 
 		IIdType id1;
 		IIdType id2;
@@ -1007,7 +1009,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			patient.addIdentifier().setSystem("ZZZZZZZ").setValue("ZZZZZZZZZ");
 			id2b = myPatientDao.update(patient, mySrd).getId();
 		}
-		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", new Object[]{id1, id2, id2b});
+		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", id1, id2, id2b);
 
 		SearchParameterMap params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
@@ -1028,7 +1030,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			// good
 		}
 
-		IBundleProvider history = myPatientDao.history((Date) null, null, mySrd);
+		IBundleProvider history = myPatientDao.history(null, null, mySrd);
 		assertEquals(4 + initialHistory, history.size().intValue());
 		List<IBaseResource> resources = history.getResources(0, 4);
 		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) resources.get(0)));
@@ -1400,7 +1402,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 
 		// By type
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(fullSize + 1, history.size().intValue());
 		for (int i = 0; i < fullSize; i++) {
 			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
@@ -1467,7 +1469,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 
 		// By type
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(fullSize + 1, history.size().intValue());
 		for (int i = 0; i < fullSize; i++) {
 			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
@@ -1524,7 +1526,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		inPatient.getMeta().addProfile("http://example.com/1");
 		IIdType id = myPatientDao.create(inPatient, mySrd).getId().toUnqualifiedVersionless();
 
-		IBundleProvider history = myPatientDao.history((Date) null, null, mySrd);
+		IBundleProvider history = myPatientDao.history(null, null, mySrd);
 		assertEquals(1, history.size().intValue());
 		Patient outPatient = (Patient) history.getResources(0, 1).get(0);
 		assertEquals("version1", inPatient.getName().get(0).getFamily());
@@ -1538,7 +1540,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		inPatient.getMeta().addProfile("http://example.com/2");
 		myPatientDao.metaAddOperation(id, inPatient.getMeta(), mySrd);
 
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(1, history.size().intValue());
 		outPatient = (Patient) history.getResources(0, 1).get(0);
 		assertEquals("version1", inPatient.getName().get(0).getFamily());
@@ -1554,7 +1556,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		inPatient.getName().get(0).setFamily("version2");
 		myPatientDao.update(inPatient, mySrd);
 
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(2, history.size().intValue());
 		outPatient = (Patient) history.getResources(0, 2).get(0);
 		assertEquals("version2", outPatient.getName().get(0).getFamily());
@@ -1582,9 +1584,9 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		IBundleProvider history = myPatientDao.history(id, null, null, mySrd);
 		List<IBaseResource> entries = history.getResources(0, 3);
-		ourLog.info(((IAnyResource) entries.get(0)).getIdElement() + " - " + ((IAnyResource) entries.get(0)).getMeta().getLastUpdated());
+		ourLog.info(entries.get(0).getIdElement() + " - " + entries.get(0).getMeta().getLastUpdated());
-		ourLog.info(((IAnyResource) entries.get(1)).getIdElement() + " - " + ((IAnyResource) entries.get(1)).getMeta().getLastUpdated());
+		ourLog.info(entries.get(1).getIdElement() + " - " + entries.get(1).getMeta().getLastUpdated());
-		ourLog.info(((IAnyResource) entries.get(2)).getIdElement() + " - " + ((IAnyResource) entries.get(2)).getMeta().getLastUpdated());
+		ourLog.info(entries.get(2).getIdElement() + " - " + entries.get(2).getMeta().getLastUpdated());
 		assertEquals(3, history.size().intValue());
 
 		assertEquals(id.withVersion("3"), entries.get(0).getIdElement());
@@ -1648,7 +1650,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		// No since
 
-		IBundleProvider history = myPatientDao.history((Date) null, null, mySrd);
+		IBundleProvider history = myPatientDao.history(null, null, mySrd);
 		assertEquals(1, history.size().intValue());
 		Patient outPatient = (Patient) history.getResources(0, 1).get(0);
 		assertEquals("version1", inPatient.getName().get(0).getFamily());
@@ -1999,7 +2001,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 				"}\n";
 		//@formatter:on
 
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		Organization org = myFhirCtx.newJsonParser().parseResource(Organization.class, inputStr);
@@ -2050,7 +2052,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		dr01.setSubject(new Reference(patientId01));
 		IIdType drId01 = myDiagnosticReportDao.create(dr01, mySrd).getId();
 
-		ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", new Object[]{patientId01, patientId02, obsId01, obsId02, drId01});
+		ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", patientId01, patientId02, obsId01, obsId02, drId01);
 
 		List<Observation> result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam(patientId01.getIdPart())).setLoadSynchronous(true)));
 		assertEquals(1, result.size());
@@ -2061,7 +2063,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		assertEquals(obsId02.getIdPart(), result.get(0).getIdElement().getIdPart());
 
 		result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));
-		;
 		assertEquals(0, result.size());
 
 	}
@@ -2145,7 +2146,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		TokenParam value = new TokenParam("urn:system", "001testPersistSearchParams");
 		List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));
-		;
 		assertEquals(1, found.size());
 		assertEquals(id, found.get(0).getIdElement().getIdPartAsLong().longValue());
 
@@ -2402,7 +2402,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			id1 = myPatientDao.create(patient, mySrd).getId();
 
 			Meta metaAdd = new Meta();
-			metaAdd.addTag().setSystem((String) null).setCode("Dog").setDisplay("Puppies");
+			metaAdd.addTag().setSystem(null).setCode("Dog").setDisplay("Puppies");
 			metaAdd.addSecurity().setSystem("seclabel:sys:1").setCode("seclabel:code:1").setDisplay("seclabel:dis:1");
 			metaAdd.addProfile("http://profile/1");
 			myPatientDao.metaAddOperation(id1, metaAdd, mySrd);
@@ -2472,7 +2472,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		{
 			Meta metaDel = new Meta();
-			metaDel.addTag().setSystem((String) null).setCode("Dog");
+			metaDel.addTag().setSystem(null).setCode("Dog");
 			metaDel.addSecurity().setSystem("seclabel:sys:1").setCode("seclabel:code:1");
 			metaDel.addProfile("http://profile/1");
 			myPatientDao.metaDeleteOperation(id1, metaDel, mySrd);
@@ -3192,7 +3192,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		assertThat(str.length(), greaterThan(ResourceIndexedSearchParamString.MAX_LENGTH));
 
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -3371,7 +3371,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		String subStr1 = longStr1.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
 		String subStr2 = longStr2.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -41,7 +42,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 	}
 
 	@Test
-	public void testCreateAndUpdateWithoutRequest() throws Exception {
+	public void testCreateAndUpdateWithoutRequest() {
 		String methodName = "testUpdateByUrl";
 
 		Patient p = new Patient();
@@ -447,9 +448,9 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 		p2.addName().setFamily("Tester").addGiven("testUpdateMaintainsSearchParamsDstu2BBB");
 		myPatientDao.create(p2, mySrd).getId();
 
-		Set<Long> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
+		Set<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
 		assertEquals(1, ids.size());
-		assertThat(ids, contains(p1id.getIdPartAsLong()));
+		assertThat(ResourcePersistentId.toLongList(ids), contains(p1id.getIdPartAsLong()));
 
 		// Update the name
 		p1.getName().get(0).getGiven().get(0).setValue("testUpdateMaintainsSearchParamsDstu2BBB");
@@ -503,7 +504,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 		{
 			Patient p1 = myPatientDao.read(p1id, mySrd);
 			List<Coding> tagList = p1.getMeta().getTag();
-			Set<String> secListValues = new HashSet<String>();
+			Set<String> secListValues = new HashSet<>();
 			for (Coding next : tagList) {
 				secListValues.add(next.getSystemElement().getValue() + "|" + next.getCodeElement().getValue());
 			}
@@ -528,7 +529,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 			Patient patient = new Patient();
 			patient.addName().setFamily(name);
 
-			List<IdType> tl = new ArrayList<IdType>();
+			List<IdType> tl = new ArrayList<>();
 			tl.add(new IdType("http://foo/bar"));
 			patient.getMeta().getProfile().addAll(tl);
 
@@ -549,7 +550,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 			patient.setId(id);
 			patient.addName().setFamily(name);
 
-			List<IdType> tl = new ArrayList<IdType>();
+			List<IdType> tl = new ArrayList<>();
 			tl.add(new IdType("http://foo/baz"));
 			patient.getMeta().getProfile().clear();
 			patient.getMeta().getProfile().addAll(tl);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSearchDaoDstu3Test.java

@@ -6,6 +6,7 @@ import static org.junit.Assert.assertThat;
 
 import java.util.List;
 
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import org.hl7.fhir.dstu3.model.Organization;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.junit.AfterClass;
@@ -65,8 +66,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// OR
 		{
@@ -74,8 +75,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}		
 		// AND
 		{
@@ -84,8 +85,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// AND OR
 		{
@@ -94,8 +95,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}
 		// All Resource Types
 		{
@@ -103,8 +104,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")).addOr(new StringParam("DDD")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(null, map);
+			List<ResourcePersistentId> found = mySearchDao.search(null, map);
-			assertThat(found, containsInAnyOrder(id1, id2, id3));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2, id3));
 		}
 
 	}
@@ -138,8 +139,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// OR
 		{
@@ -147,8 +148,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}		
 		// AND
 		{
@@ -157,8 +158,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// AND OR
 		{
@@ -167,8 +168,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}
 		// Tag Contents
 		{
@@ -176,8 +177,8 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("div")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, empty());
+			assertThat(ResourcePersistentId.toLongList(found), empty());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -22,7 +22,7 @@ import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
-import ca.uhn.fhir.jpa.searchparam.registry.BaseSearchParamRegistry;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
 import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
@@ -277,7 +277,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("mySearchParameterDaoR4")
 	protected IFhirResourceDao<SearchParameter> mySearchParameterDao;
 	@Autowired
-	protected BaseSearchParamRegistry mySearchParamRegistry;
+	protected SearchParamRegistryImpl mySearchParamRegistry;
 	@Autowired
 	protected IStaleSearchDeletingSvc myStaleSearchDeletingSvc;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java

@@ -19,6 +19,7 @@ import org.junit.Test;
 
 import java.util.List;
 
+import static org.hamcrest.CoreMatchers.startsWith;
 import static org.hamcrest.Matchers.contains;
 import static org.junit.Assert.*;
 
@@ -43,7 +44,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 			myObservationDao.create(o, mySrd);
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Resource Patient/FOO not found, specified in path: Observation.subject", e.getMessage());
+			assertThat(e.getMessage(), startsWith("Resource Patient/FOO not found, specified in path: Observation.subject"));
 		}
 	}
 
@@ -98,7 +99,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 			myObservationDao.update(o, mySrd);
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Resource Patient/FOO not found, specified in path: Observation.subject", e.getMessage());
+			assertThat(e.getMessage(), startsWith("Resource Patient/FOO not found, specified in path: Observation.subject"));
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4DeleteTest.java

@@ -32,12 +32,14 @@ public class FhirResourceDaoR4DeleteTest extends BaseJpaR4Test {
 		runInTransaction(()->{
 			ResourceTable resourceTable = myResourceTableDao.findById(id.getIdPartAsLong()).get();
 			assertNotNull(resourceTable.getDeleted());
+			assertTrue(resourceTable.isDeleted());
 		});
 
 		// Current version should be marked as deleted
 		runInTransaction(()->{
 			ResourceHistoryTable resourceTable = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id.getIdPartAsLong(), 1);
 			assertNull(resourceTable.getDeleted());
+			assertNotNull(resourceTable.getPersistentId());
 		});
 		runInTransaction(()->{
 			ResourceHistoryTable resourceTable = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id.getIdPartAsLong(), 2);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -3867,6 +3867,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		result = myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ValueSet.SP_URL, new UriParam("http://hl7.org/fhir/ValueSet/FOOOOOO")));
 		assertThat(toUnqualifiedVersionlessIds(result), empty());
 
+
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchTest.java

@@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 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.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@@ -181,7 +182,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchTest extends BaseJpaTest {
 		TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
 		parentC.addChild(childCA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		return codeSystem;
 	}
 
@@ -199,7 +200,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchTest extends BaseJpaTest {
 	}
 
 	private ArrayList<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
-		ArrayList<String> retVal = new ArrayList<String>();
+		ArrayList<String> retVal = new ArrayList<>();
 		for (ValueSet.ValueSetExpansionContainsComponent next : theContains) {
 			retVal.add(next.getCode());
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
@@ -95,7 +96,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
 		parentC.addChild(childCA, RelationshipTypeEnum.ISA);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		return codeSystem;
 	}
 
@@ -131,7 +132,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
 		dogs.addChild(beagle, RelationshipTypeEnum.ISA);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		return codeSystem;
 	}
 
@@ -162,7 +163,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 			parentB.addChild(childI, RelationshipTypeEnum.ISA);
 		}
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 	}
 
 	private void createLocalCsAndVs() {
@@ -474,7 +475,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		concept = new TermConcept(cs, "LA9999-7");
 		cs.getConcepts().add(concept);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
 
 		ValueSet valueSet = new ValueSet();
 		valueSet.setUrl(URL_MY_VALUE_SET);
@@ -801,7 +802,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		cs.setResource(table);
 		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
 		cs.getConcepts().add(parentA);
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), "http://snomed.info/sct", "Snomed CT", "SYSTEM VERSION" , cs, table);
 
 		StringType code = new StringType("ParentA");
 		StringType system = new StringType("http://snomed.info/sct");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.*;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
@@ -317,12 +318,12 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		IIdType id2 = myObservationDao.create(o2, mySrd).getId();
 
 		{
-			Set<Long> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
+			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2001-01-02")), null);
-			assertThat(found, hasItem(id2.getIdPartAsLong()));
+			assertThat(ResourcePersistentId.toLongList(found), hasItem(id2.getIdPartAsLong()));
 		}
 		{
-			Set<Long> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
+			Set<ResourcePersistentId> found = myObservationDao.searchForIds(new SearchParameterMap(Observation.SP_DATE, new DateParam(">2016-01-02")), null);
-			assertThat(found, not(hasItem(id2.getIdPartAsLong())));
+			assertThat(ResourcePersistentId.toLongList(found), not(hasItem(id2.getIdPartAsLong())));
 		}
 	}
 
@@ -2297,7 +2298,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 				"}\n";
 		//@formatter:on
 
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		Organization org = myFhirCtx.newJsonParser().parseResource(Organization.class, inputStr);
@@ -3592,7 +3593,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		assertThat(str.length(), greaterThan(ResourceIndexedSearchParamString.MAX_LENGTH));
 
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);
@@ -3771,7 +3772,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		String subStr1 = longStr1.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
 		String subStr2 = longStr2.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH);
-		Set<Long> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
+		Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("type", new TokenParam(subStr1, subStr2)), null);
 		int initial = val.size();
 
 		myOrganizationDao.create(org, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -568,9 +569,9 @@ public class FhirResourceDaoR4UpdateTest extends BaseJpaR4Test {
 		p2.addName().setFamily("Tester").addGiven("testUpdateMaintainsSearchParamsDstu2BBB");
 		myPatientDao.create(p2, mySrd).getId();
 
-		Set<Long> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
+		Set<ResourcePersistentId> ids = myPatientDao.searchForIds(new SearchParameterMap(Patient.SP_GIVEN, new StringParam("testUpdateMaintainsSearchParamsDstu2AAA")), null);
 		assertEquals(1, ids.size());
-		assertThat(ids, contains(p1id.getIdPartAsLong()));
+		assertThat(ResourcePersistentId.toLongList(ids), contains(p1id.getIdPartAsLong()));
 
 		// Update the name
 		p1.getName().get(0).getGiven().get(0).setValue("testUpdateMaintainsSearchParamsDstu2BBB");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSearchDaoR4Test.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.StringAndListParam;
@@ -66,8 +67,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// OR
 		{
@@ -75,8 +76,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}		
 		// AND
 		{
@@ -85,8 +86,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// AND OR
 		{
@@ -95,8 +96,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}
 		// All Resource Types
 		{
@@ -104,8 +105,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")).addOr(new StringParam("DDD")));
 			
 			map.add(Constants.PARAM_CONTENT, content);
-			List<Long> found = mySearchDao.search(null, map);
+			List<ResourcePersistentId> found = mySearchDao.search(null, map);
-			assertThat(found, containsInAnyOrder(id1, id2, id3));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2, id3));
 		}
 
 	}
@@ -139,8 +140,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// OR
 		{
@@ -148,8 +149,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}		
 		// AND
 		{
@@ -158,8 +159,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
 		}
 		// AND OR
 		{
@@ -168,8 +169,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, containsInAnyOrder(id1, id2));
+			assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
 		}
 		// Tag Contents
 		{
@@ -177,8 +178,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
 			content.addAnd(new StringOrListParam().addOr(new StringParam("div")));
 			
 			map.add(Constants.PARAM_TEXT, content);
-			List<Long> found = mySearchDao.search(resourceName, map);
+			List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
-			assertThat(found, empty());
+			assertThat(ResourcePersistentId.toLongList(found), empty());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4Test.java

@@ -3,8 +3,12 @@ package ca.uhn.fhir.jpa.dao.r4;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
-import ca.uhn.fhir.jpa.model.entity.*;
+import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
 import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
+import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
 import ca.uhn.fhir.jpa.searchparam.extractor.PathAndRef;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
@@ -13,7 +17,15 @@ import ca.uhn.fhir.util.TestUtil;
 import com.google.common.collect.Sets;
 import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Consent;
+import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Quantity;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.SearchParameter;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -21,7 +33,13 @@ import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import static org.junit.Assert.assertEquals;
@@ -32,7 +50,7 @@ public class SearchParamExtractorR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(SearchParamExtractorR4Test.class);
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static IValidationSupport ourValidationSupport;
-	private ISearchParamRegistry mySearchParamRegistry;
+	private MySearchParamRegistry mySearchParamRegistry;
 
 	@Before
 	public void before() {
@@ -77,10 +95,11 @@ public class SearchParamExtractorR4Test {
 		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
 		RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam("Encounter", "location");
 		assertNotNull(param);
-		List<PathAndRef> links = extractor.extractResourceLinks(enc, param);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(enc);
 		assertEquals(1, links.size());
-		assertEquals("Encounter.location.location", links.get(0).getPath());
+		assertEquals("location", links.iterator().next().getSearchParamName());
-		assertEquals("Location/123", ((Reference) links.get(0).getRef()).getReference());
+		assertEquals("Encounter.location.location", links.iterator().next().getPath());
+		assertEquals("Location/123", ((Reference) links.iterator().next().getRef()).getReference());
 	}
 
 	@Test
@@ -91,10 +110,10 @@ public class SearchParamExtractorR4Test {
 		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
 		RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam("Consent", Consent.SP_SOURCE_REFERENCE);
 		assertNotNull(param);
-		List<PathAndRef> links = extractor.extractResourceLinks(consent, param);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(consent);
 		assertEquals(1, links.size());
-		assertEquals("Consent.source", links.get(0).getPath());
+		assertEquals("Consent.source", links.iterator().next().getPath());
-		assertEquals("Consent/999", ((Reference) links.get(0).getRef()).getReference());
+		assertEquals("Consent/999", ((Reference) links.iterator().next().getRef()).getReference());
 	}
 
 
@@ -103,13 +122,15 @@ public class SearchParamExtractorR4Test {
 		String path = "Patient.extension('http://patext').value.as(Reference)";
 
 		RuntimeSearchParam sp = new RuntimeSearchParam("extpat", "Patient SP", path, RestSearchParameterTypeEnum.REFERENCE, new HashSet<>(), Sets.newHashSet("Patient"), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE);
+		mySearchParamRegistry.addSearchParam(sp);
 
 		Patient patient = new Patient();
 		patient.addExtension("http://patext", new Reference("Organization/AAA"));
 
 		SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), ourCtx, ourValidationSupport, mySearchParamRegistry);
-		List<PathAndRef> links = extractor.extractResourceLinks(patient, sp);
+		ISearchParamExtractor.SearchParamSet<PathAndRef> links = extractor.extractResourceLinks(patient);
 		assertEquals(1, links.size());
+
 	}
 
 	@Test
@@ -129,6 +150,10 @@ public class SearchParamExtractorR4Test {
 	}
 
 	private static class MySearchParamRegistry implements ISearchParamRegistry {
+
+
+		private List<RuntimeSearchParam> myExtraSearchParams = new ArrayList<>();
+
 		@Override
 		public void forceRefresh() {
 			// nothing
@@ -158,9 +183,17 @@ public class SearchParamExtractorR4Test {
 				sps.put(nextSp.getName(), nextSp);
 			}
 
+			for (RuntimeSearchParam next : myExtraSearchParams) {
+				sps.put(next.getName(), next);
+			}
+
 			return sps;
 		}
 
+		public void addSearchParam(RuntimeSearchParam theSearchParam) {
+			myExtraSearchParams.add(theSearchParam);
+		}
+
 		@Override
 		public List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName, Set<String> theParamNames) {
 			throw new UnsupportedOperationException();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java

@@ -19,7 +19,7 @@ import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
-import ca.uhn.fhir.jpa.searchparam.registry.BaseSearchParamRegistry;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
 import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
@@ -261,7 +261,7 @@ public abstract class BaseJpaR5Test extends BaseJpaTest {
 	@Qualifier("mySearchParameterDaoR5")
 	protected IFhirResourceDao<SearchParameter> mySearchParameterDao;
 	@Autowired
-	protected BaseSearchParamRegistry mySearchParamRegistry;
+	protected SearchParamRegistryImpl mySearchParamRegistry;
 	@Autowired
 	protected IStaleSearchDeletingSvc myStaleSearchDeletingSvc;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java

@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu3;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.parser.StrictErrorHandler;
@@ -58,7 +58,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 	protected static RestfulServer ourRestServer;
 	protected static String ourServerBase;
 	protected static GenericWebApplicationContext ourWebApplicationContext;
-	protected static SearchParamRegistryDstu3 ourSearchParamRegistry;
+	protected static SearchParamRegistryImpl ourSearchParamRegistry;
 	protected static DatabaseBackedPagingProvider ourPagingProvider;
 	protected static ISearchCoordinatorSvc ourSearchCoordinatorSvc;
 	private static Server ourServer;
@@ -153,7 +153,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			WebApplicationContext wac = WebApplicationContextUtils.getWebApplicationContext(subsServletHolder.getServlet().getServletConfig().getServletContext());
 			myValidationSupport = wac.getBean(JpaValidationSupportChainDstu3.class);
 			ourSearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
-			ourSearchParamRegistry = wac.getBean(SearchParamRegistryDstu3.class);
+			ourSearchParamRegistry = wac.getBean(SearchParamRegistryImpl.class);
 			ourSubscriptionTriggeringProvider = wac.getBean(SubscriptionTriggeringProvider.class);
 
 			myFhirCtx.getRestfulClientFactory().setSocketTimeout(5000000);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -151,7 +152,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 			code.addPropertyString("HELLO", "12345-2");
 			cs.getConcepts().add(code);
 
-			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		});
 	}
 
@@ -849,7 +850,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
 		cs.getConcepts().add(parentB);
 
-		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		return codeSystem;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java

@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.subscription.SubscriptionMatcherInterceptor;
 import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionLoader;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
@@ -61,7 +61,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 	protected static int ourPort;
 	protected static RestfulServer ourRestServer;
 	protected static String ourServerBase;
-	protected static SearchParamRegistryR4 ourSearchParamRegistry;
+	protected static SearchParamRegistryImpl ourSearchParamRegistry;
 	private static DatabaseBackedPagingProvider ourPagingProvider;
 	protected static ISearchCoordinatorSvc mySearchCoordinatorSvc;
 	private static GenericWebApplicationContext ourWebApplicationContext;
@@ -163,7 +163,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 			WebApplicationContext wac = WebApplicationContextUtils.getWebApplicationContext(subsServletHolder.getServlet().getServletConfig().getServletContext());
 			myValidationSupport = wac.getBean(JpaValidationSupportChainR4.class);
 			mySearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
-			ourSearchParamRegistry = wac.getBean(SearchParamRegistryR4.class);
+			ourSearchParamRegistry = wac.getBean(SearchParamRegistryImpl.class);
 			ourSubscriptionMatcherInterceptor = wac.getBean(SubscriptionMatcherInterceptor.class);
 			ourSubscriptionMatcherInterceptor.start();
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -37,13 +38,16 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.persistence.Query;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.in;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
@@ -59,15 +63,14 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	@After
 	public void after() throws Exception {
 		super.after();
-
 		myModelConfig.setDefaultSearchParamsCanBeOverridden(new ModelConfig().isDefaultSearchParamsCanBeOverridden());
 		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
-
 	}
 
 	@Override
 	public void before() throws Exception {
 		super.before();
+		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
 	}
 
 	@Override
@@ -462,8 +465,6 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 		Interceptor interceptor = new Interceptor();
 		myInterceptorRegistry.registerInterceptor(interceptor);
 		try {
-			myDaoConfig.setAllowContainsSearches(true);
-
 			// Add a custom search parameter
 			SearchParameter fooSp = new SearchParameter();
 			fooSp.addBase("Questionnaire");
@@ -520,6 +521,8 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 				ids.add(myQuestionnaireDao.create(q).getId().getIdPartAsLong());
 			}
 
+			myCaptureQueriesListener.clear();
+
 			int foundCount = 0;
 			Bundle bundle = null;
 			List<Long> actualIds = new ArrayList<>();
@@ -543,17 +546,42 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 
 			} while (bundle.getLink("next") != null);
 
+			String queries = " * " + myCaptureQueriesListener
+				.getSelectQueries()
+				.stream()
+				.map(t->t.getSql(true, false))
+				.collect(Collectors.joining("\n * "));
+
 			ourLog.info("Found: {}", found);
 
 			runInTransaction(() -> {
 
+				List currentResults = myEntityManager.createNativeQuery("select distinct resourceta0_.RES_ID as col_0_0_ from HFJ_RESOURCE resourceta0_ left outer join HFJ_SPIDX_STRING myparamsst1_ on resourceta0_.RES_ID=myparamsst1_.RES_ID where myparamsst1_.HASH_NORM_PREFIX='5901791607832193956' and (myparamsst1_.SP_VALUE_NORMALIZED like 'SECTION%') limit '500'")					.getResultList();
+				List currentResources = myEntityManager.createNativeQuery("select resourceta0_.RES_ID as col_0_0_ from HFJ_RESOURCE resourceta0_")					.getResultList();
+
 				List<Search> searches = mySearchEntityDao.findAll();
 				assertEquals(1, searches.size());
 				Search search = searches.get(0);
-				String message = "\nWanted: " + (ids) + "\n" +
+				String message = "\nWanted : " + (ids) + "\n" +
-					"Actual: " + (actualIds) + "\n" +
+					"Actual : " + (actualIds) + "\n" +
-					"Found : " + (found) + "\n" +
+					"Found  : " + (found) + "\n" +
-					search.toString();
+					"Current: " + currentResults + "\n" +
+					"Current: " + currentResources + "\n" +
+					search.toString() +
+					"\nQueries :\n" + queries;
+
+				for (Long next :ids) {
+					if (!actualIds.contains(next)) {
+						List<ResourceIndexedSearchParamString> indexes = myResourceIndexedSearchParamStringDao
+							.findAll()
+							.stream()
+							.filter(t->t.getResourcePid().equals(next))
+							.collect(Collectors.toList());
+						message += "\n\nResource " + next + " has prefixes:\n * " + indexes.stream().map(t->t.toString()).collect(Collectors.joining("\n * "));
+						break;
+					}
+				}
+
 				assertEquals(message, 200, search.getNumFound());
 				assertEquals(message, 200, search.getTotalCount().intValue());
 				assertEquals(message, SearchStatusEnum.FINISHED, search.getStatus());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -1053,7 +1054,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
 		cs.getConcepts().add(parentB);
 
-		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
 		return codeSystem;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java

@@ -14,6 +14,7 @@ import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
 import ca.uhn.fhir.rest.gclient.IClientExecutable;
 import ca.uhn.fhir.rest.gclient.IQuery;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.r4.model.Bundle;
@@ -24,6 +25,7 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.util.AopTestUtils;
 
 import java.util.Date;
@@ -33,6 +35,11 @@ import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 
+@TestPropertySource(properties = {
+	// Since scheduled tasks can cause searches, which messes up the
+	// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
+	UnregisterScheduledProcessor.SCHEDULING_DISABLED_EQUALS_TRUE
+})
 public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StaleSearchDeletingSvcR4Test.class);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/BaseResourceProviderR5Test.java

@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
-import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR5;
+import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
 import ca.uhn.fhir.jpa.subscription.SubscriptionMatcherInterceptor;
 import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionLoader;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
@@ -61,7 +61,7 @@ public abstract class BaseResourceProviderR5Test extends BaseJpaR5Test {
 	protected static int ourPort;
 	protected static RestfulServer ourRestServer;
 	protected static String ourServerBase;
-	protected static SearchParamRegistryR5 ourSearchParamRegistry;
+	protected static SearchParamRegistryImpl ourSearchParamRegistry;
 	private static DatabaseBackedPagingProvider ourPagingProvider;
 	protected static ISearchCoordinatorSvc mySearchCoordinatorSvc;
 	private static GenericWebApplicationContext ourWebApplicationContext;
@@ -164,7 +164,7 @@ public abstract class BaseResourceProviderR5Test extends BaseJpaR5Test {
 			WebApplicationContext wac = WebApplicationContextUtils.getWebApplicationContext(subsServletHolder.getServlet().getServletConfig().getServletContext());
 			myValidationSupport = wac.getBean(JpaValidationSupportChainR5.class);
 			mySearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
-			ourSearchParamRegistry = wac.getBean(SearchParamRegistryR5.class);
+			ourSearchParamRegistry = wac.getBean(SearchParamRegistryImpl.class);
 			ourSubscriptionMatcherInterceptor = wac.getBean(SubscriptionMatcherInterceptor.class);
 			ourSubscriptionMatcherInterceptor.start();
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
@@ -1063,7 +1064,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
 		cs.getConcepts().add(parentB);
 
-		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+		theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
 		return codeSystem;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
 import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
@@ -110,19 +111,19 @@ public class SearchCoordinatorSvcImplTest {
 		}).when(myCallingDao).injectDependenciesIntoBundleProvider(any(PersistedJpaBundleProvider.class));
 	}
 
-	private List<Long> createPidSequence(int to) {
+	private List<ResourcePersistentId> createPidSequence(int to) {
-		List<Long> pids = new ArrayList<>();
+		List<ResourcePersistentId> pids = new ArrayList<>();
 		for (long i = 10; i < to; i++) {
-			pids.add(i);
+			pids.add(new ResourcePersistentId(i));
 		}
 		return pids;
 	}
 
 	private Answer<Void> loadPids() {
 		return theInvocation -> {
-			List<Long> pids = (List<Long>) theInvocation.getArguments()[0];
+			List<ResourcePersistentId> pids = (List<ResourcePersistentId>) theInvocation.getArguments()[0];
 			List<IBaseResource> resources = (List<IBaseResource>) theInvocation.getArguments()[2];
-			for (Long nextPid : pids) {
+			for (ResourcePersistentId nextPid : pids) {
 				Patient pt = new Patient();
 				pt.setId(nextPid.toString());
 				resources.add(pt);
@@ -136,7 +137,7 @@ public class SearchCoordinatorSvcImplTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		IResultIterator iter = new FailAfterNIterator(new SlowIterator(pids.iterator(), 2), 300);
 		when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
 
@@ -154,10 +155,10 @@ public class SearchCoordinatorSvcImplTest {
 
 	@Test
 	public void testAsyncSearchLargeResultSetBigCountSameCoordinator() {
-		List<Long> allResults = new ArrayList<>();
+		List<ResourcePersistentId> allResults = new ArrayList<>();
 		doAnswer(t -> {
-			List<Long> oldResults = t.getArgument(1, List.class);
+			List<ResourcePersistentId> oldResults = t.getArgument(1, List.class);
-			List<Long> newResults = t.getArgument(2, List.class);
+			List<ResourcePersistentId> newResults = t.getArgument(2, List.class);
 			ourLog.info("Saving {} new results - have {} old results", newResults.size(), oldResults.size());
 			assertEquals(allResults.size(), oldResults.size());
 			allResults.addAll(newResults);
@@ -168,13 +169,13 @@ public class SearchCoordinatorSvcImplTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		SlowIterator iter = new SlowIterator(pids.iterator(), 1);
 		when(mySearchBuilder.createQuery(any(), any(), any())).thenReturn(iter);
 		doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
 
 		when(mySearchResultCacheSvc.fetchResultPids(any(), anyInt(), anyInt())).thenAnswer(t -> {
-			List<Long> returnedValues = iter.getReturnedValues();
+			List<ResourcePersistentId> returnedValues = iter.getReturnedValues();
 			int offset = t.getArgument(1, Integer.class);
 			int end = t.getArgument(2, Integer.class);
 			end = Math.min(end, returnedValues.size());
@@ -218,8 +219,8 @@ public class SearchCoordinatorSvcImplTest {
 		verify(mySearchCacheSvc, atLeastOnce()).save(searchCaptor.capture());
 
 		assertEquals(790, allResults.size());
-		assertEquals(10, allResults.get(0).longValue());
+		assertEquals(10, allResults.get(0).getIdAsLong().longValue());
-		assertEquals(799, allResults.get(789).longValue());
+		assertEquals(799, allResults.get(789).getIdAsLong().longValue());
 
 		myExpectedNumberOfSearchBuildersCreated = 4;
 	}
@@ -274,7 +275,7 @@ public class SearchCoordinatorSvcImplTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		SlowIterator iter = new SlowIterator(pids.iterator(), 2);
 		when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
 
@@ -298,7 +299,7 @@ public class SearchCoordinatorSvcImplTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		SlowIterator iter = new SlowIterator(pids.iterator(), 500);
 		when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
 
@@ -342,7 +343,7 @@ public class SearchCoordinatorSvcImplTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		IResultIterator iter = new SlowIterator(pids.iterator(), 2);
 		when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
 		when(mySearchCacheSvc.save(any())).thenAnswer(t -> t.getArguments()[0]);
@@ -387,7 +388,7 @@ public class SearchCoordinatorSvcImplTest {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(100);
+		List<ResourcePersistentId> pids = createPidSequence(100);
 		SlowIterator iter = new SlowIterator(pids.iterator(), 2);
 		when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
 
@@ -435,9 +436,10 @@ public class SearchCoordinatorSvcImplTest {
 			}
 
 			when(mySearchResultCacheSvc.fetchResultPids(any(Search.class), anyInt(), anyInt())).thenAnswer(theInvocation -> {
-				ArrayList<Long> results = new ArrayList<>();
+				ArrayList<ResourcePersistentId> results = new ArrayList<>();
 				for (long i = theInvocation.getArgument(1, Integer.class); i < theInvocation.getArgument(2, Integer.class); i++) {
-					results.add(i + 10L);
+					Long nextPid = i + 10L;
+					results.add(new ResourcePersistentId(nextPid));
 				}
 
 				return results;
@@ -470,7 +472,7 @@ public class SearchCoordinatorSvcImplTest {
 		params.setLoadSynchronous(true);
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(new ResultIterator(pids.iterator()));
 
 		doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
@@ -491,7 +493,7 @@ public class SearchCoordinatorSvcImplTest {
 		params.setLoadSynchronousUpTo(100);
 		params.add("name", new StringParam("ANAME"));
 
-		List<Long> pids = createPidSequence(800);
+		List<ResourcePersistentId> pids = createPidSequence(800);
 		when(mySearchBuilder.createQuery(same(params), any(), nullable(RequestDetails.class))).thenReturn(new ResultIterator(pids.iterator()));
 
 		pids = createPidSequence(110);
@@ -563,7 +565,7 @@ public class SearchCoordinatorSvcImplTest {
 
 	}
 
-	public static class FailAfterNIterator extends BaseIterator<Long> implements IResultIterator {
+	public static class FailAfterNIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
 
 		private int myCount;
 		private IResultIterator myWrap;
@@ -579,7 +581,7 @@ public class SearchCoordinatorSvcImplTest {
 		}
 
 		@Override
-		public Long next() {
+		public ResourcePersistentId next() {
 			myCount--;
 			if (myCount == 0) {
 				throw new NullPointerException("FAILED");
@@ -598,11 +600,11 @@ public class SearchCoordinatorSvcImplTest {
 		}
 	}
 
-	public static class ResultIterator extends BaseIterator<Long> implements IResultIterator {
+	public static class ResultIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
 
-		private final Iterator<Long> myWrap;
+		private final Iterator<ResourcePersistentId> myWrap;
 
-		ResultIterator(Iterator<Long> theWrap) {
+		ResultIterator(Iterator<ResourcePersistentId> theWrap) {
 			myWrap = theWrap;
 		}
 
@@ -612,7 +614,7 @@ public class SearchCoordinatorSvcImplTest {
 		}
 
 		@Override
-		public Long next() {
+		public ResourcePersistentId next() {
 			return myWrap.next();
 		}
 
@@ -633,22 +635,22 @@ public class SearchCoordinatorSvcImplTest {
 	 * <p>
 	 * Don't use it in real code!
 	 */
-	public static class SlowIterator extends BaseIterator<Long> implements IResultIterator {
+	public static class SlowIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
 
 		private static final Logger ourLog = LoggerFactory.getLogger(SlowIterator.class);
 		private final IResultIterator myResultIteratorWrap;
 		private int myDelay;
-		private Iterator<Long> myWrap;
+		private Iterator<ResourcePersistentId> myWrap;
-		private List<Long> myReturnedValues = new ArrayList<>();
+		private List<ResourcePersistentId> myReturnedValues = new ArrayList<>();
 		private AtomicInteger myCountReturned = new AtomicInteger(0);
 
-		SlowIterator(Iterator<Long> theWrap, int theDelay) {
+		SlowIterator(Iterator<ResourcePersistentId> theWrap, int theDelay) {
 			myWrap = theWrap;
 			myDelay = theDelay;
 			myResultIteratorWrap = null;
 		}
 
-		List<Long> getReturnedValues() {
+		List<ResourcePersistentId> getReturnedValues() {
 			return myReturnedValues;
 		}
 
@@ -666,13 +668,13 @@ public class SearchCoordinatorSvcImplTest {
 		}
 
 		@Override
-		public Long next() {
+		public ResourcePersistentId next() {
 			try {
 				Thread.sleep(myDelay);
 			} catch (InterruptedException e) {
 				// ignore
 			}
-			Long retVal = myWrap.next();
+			ResourcePersistentId retVal = myWrap.next();
 			myReturnedValues.add(retVal);
 			myCountReturned.incrementAndGet();
 			return retVal;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/BaseTermR4Test.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
 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.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeSystem;
@@ -90,7 +91,7 @@ public abstract class BaseTermR4Test extends BaseJpaR4Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB");
 		cs.getConcepts().add(parentB);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 
 		return id;
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java

@@ -7,6 +7,7 @@ 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.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -97,7 +98,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermConcept parentB = new TermConcept(cs, "ParentB");
 		cs.getConcepts().add(parentB);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 
 		return id;
 	}
@@ -116,7 +117,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermConcept parentA = new TermConcept(cs, "CS2");
 		cs.getConcepts().add(parentA);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), CS_URL_2, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL_2, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 
 	}
 
@@ -185,7 +186,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 				code2.getDisplay());
 			cs.getConcepts().add(code4);
 
-			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), LOINC_URI, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), LOINC_URI, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 		});
 	}
 
@@ -201,7 +202,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);
 
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 
 		// Update
 		cs = new TermCodeSystemVersion();
@@ -210,7 +211,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		id = myCodeSystemDao.update(codeSystem, null, true, true, mySrd).getId().toUnqualified();
 		table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
 		cs.setResource(table);
-		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 
 		// Try to update to a different resource
 		codeSystem = new CodeSystem();
@@ -1780,7 +1781,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		child.addChild(parent, RelationshipTypeEnum.ISA);
 
 		try {
-			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION", cs, table);
 			fail();
 		} catch (InvalidRequestException e) {
 			assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
@@ -1905,7 +1906,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		runInTransaction(() -> {
 			ResourceTable resTable = myEntityManager.find(ResourceTable.class, csId.getIdPartAsLong());
 			version.setResource(resTable);
-			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", "SYSTEM VERSION", version, resTable);
+			myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(csId.getIdPartAsLong()), cs.getUrl(), "My System", "SYSTEM VERSION", version, resTable);
 		});
 
 		org.hl7.fhir.dstu3.model.ValueSet vs = new org.hl7.fhir.dstu3.model.ValueSet();

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/cross/IBasePersistedResource.java

@@ -0,0 +1,40 @@
+package ca.uhn.fhir.jpa.model.cross;
+
+/*-
+ * #%L
+ * HAPI FHIR Model
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import java.util.Date;
+
+public interface IBasePersistedResource {
+
+	IIdType getIdDt();
+
+	boolean isDeleted();
+
+	/**
+	 * If the resource is deleted, returns the date/time that the resource was deleted at. Otherwie, returns <code>null</code>
+	 */
+	Date getDeleted();
+
+	ResourcePersistentId getPersistentId();
+
+}

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/cross/ResourcePersistentId.java

@@ -0,0 +1,88 @@
+package ca.uhn.fhir.jpa.model.cross;
+
+/*-
+ * #%L
+ * HAPI FHIR Model
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.util.ObjectUtil;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+/**
+ * This class is an abstraction for however primary keys are stored in the underlying storage engine. This might be
+ * a Long, a String, or something else.
+ */
+public class ResourcePersistentId {
+
+	private Object myId;
+
+	public ResourcePersistentId(Object theId) {
+		myId = theId;
+	}
+
+	@Override
+	public boolean equals(Object theO) {
+		if (!(theO instanceof ResourcePersistentId)) {
+			return false;
+		}
+		ResourcePersistentId that = (ResourcePersistentId) theO;
+
+		return ObjectUtil.equals(myId, that.myId);
+	}
+
+	@Override
+	public int hashCode() {
+		return myId.hashCode();
+	}
+
+	public Object getId() {
+		return myId;
+	}
+
+	public void setId(Object theId) {
+		myId = theId;
+	}
+
+	public Long getIdAsLong() {
+		return (Long) myId;
+	}
+
+	@Override
+	public String toString() {
+		return myId.toString();
+	}
+
+	public static List<Long> toLongList(Collection<ResourcePersistentId> thePids) {
+		List<Long> retVal = new ArrayList<>(thePids.size());
+		for (ResourcePersistentId next : thePids) {
+			retVal.add(next.getIdAsLong());
+		}
+		return retVal;
+	}
+
+	public static List<ResourcePersistentId> fromLongList(List<Long> theResultList) {
+		List<ResourcePersistentId> retVal = new ArrayList<>(theResultList.size());
+		for (Long next : theResultList) {
+			retVal.add(new ResourcePersistentId(next));
+		}
+		return retVal;
+	}
+}

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BaseHasResource.java

@@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.model.entity;
  */
 
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.Constants;
@@ -31,7 +33,7 @@ import java.util.Collection;
 import java.util.Date;
 
 @MappedSuperclass
-public abstract class BaseHasResource implements IBaseResourceEntity {
+public abstract class BaseHasResource implements IBaseResourceEntity, IBasePersistedResource {
 
 	@Column(name = "RES_DELETED_AT", nullable = true)
 	@Temporal(TemporalType.TIMESTAMP)
@@ -85,10 +87,6 @@ public abstract class BaseHasResource implements IBaseResourceEntity {
 		return cloneDate(myDeleted);
 	}
 
-	public void setDeleted(Date theDate) {
-		myDeleted = theDate;
-	}
-
 	@Override
 	public FhirVersionEnum getFhirVersion() {
 		return myFhirVersion;
@@ -121,6 +119,15 @@ public abstract class BaseHasResource implements IBaseResourceEntity {
 		}
 	}
 
+	@Override
+	public boolean isDeleted() {
+		return myDeleted != null;
+	}
+
+	public void setDeleted(Date theDate) {
+		myDeleted = theDate;
+	}
+
 	@Override
 	public InstantDt getPublished() {
 		if (myPublished != null) {

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ModelConfig.java

@@ -61,6 +61,13 @@ public class ModelConfig {
 	private boolean mySubscriptionMatchingEnabled = true;
 	private String myWebsocketContextPath = DEFAULT_WEBSOCKET_CONTEXT_PATH;
 
+	/**
+	 * Constructor
+	 */
+	public ModelConfig() {
+		super();
+	}
+
 	/**
 	 * If set to {@code true} the default search params (i.e. the search parameters that are
 	 * defined by the FHIR specification itself) may be overridden by uploading search