Issue 2332 create via put for implementationguide that references some placeholders (#2423)

* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback

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

@@ -32,6 +32,7 @@ import org.apache.jena.riot.Lang;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
@@ -103,7 +104,7 @@ public class FhirContext {
 	private AddProfileTagEnum myAddProfileTagWhenEncoding = AddProfileTagEnum.ONLY_FOR_CUSTOM;
 	private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition = Collections.emptyMap();
 	private ArrayList<Class<? extends IBase>> myCustomTypes;
-	private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<>();
+	private final Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<>();
 	private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
 	private volatile boolean myInitialized;
 	private volatile boolean myInitializing = false;
@@ -114,8 +115,8 @@ public class FhirContext {
 	private volatile INarrativeGenerator myNarrativeGenerator;
 	private volatile IParserErrorHandler myParserErrorHandler = new LenientErrorHandler();
 	private ParserOptions myParserOptions = new ParserOptions();
-	private Set<PerformanceOptionsEnum> myPerformanceOptions = new HashSet<>();
+	private final Set<PerformanceOptionsEnum> myPerformanceOptions = new HashSet<>();
-	private Collection<Class<? extends IBaseResource>> myResourceTypesToScan;
+	private final Collection<Class<? extends IBaseResource>> myResourceTypesToScan;
 	private volatile IRestfulClientFactory myRestfulClientFactory;
 	private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
 	private IValidationSupport myValidationSupport;
@@ -1066,4 +1067,10 @@ public class FhirContext {
 		return retVal;
 	}
 
+	// TODO KHS add the other primitive types
+	public IPrimitiveType<Boolean> getPrimitiveBoolean(Boolean theValue) {
+		IPrimitiveType<Boolean> retval = (IPrimitiveType<Boolean>) getElementDefinition("boolean").newInstance();
+		retval.setValue(theValue);
+		return retval;
+	}
 }

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

@@ -101,6 +101,17 @@ public class HapiExtensions {
 	public static final String EXT_META_SOURCE = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-source";
 	public static final String EXT_SP_UNIQUE = "http://hapifhir.io/fhir/StructureDefinition/sp-unique";
 
+	/**
+	 * URL for extension on a Phonetic String SearchParameter indicating that text values should be phonetically indexed with the named encoder
+	 */
+	public static final String EXT_SEARCHPARAM_PHONETIC_ENCODER = "http://hapifhir.io/fhir/StructureDefinition/searchparameter-phonetic-encoder";
+
+	/**
+	 * URL for boolean extension added to all placeholder resources
+	 */
+	public static final String EXT_RESOURCE_META_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder";
+
+
 	/**
 	 * Non instantiable
 	 */

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

@@ -80,10 +80,7 @@ public class ParametersUtil {
 					.filter(t -> t instanceof IPrimitiveType<?>)
 					.map(t -> ((IPrimitiveType<?>) t))
 					.findFirst();
-				if (!nameValue.isPresent() || !theParameterName.equals(nameValue.get().getValueAsString())) {
+				return nameValue.isPresent() && theParameterName.equals(nameValue.get().getValueAsString());
-					return false;
-				}
-				return true;
 			})
 			.collect(Collectors.toList());
 
@@ -227,9 +224,7 @@ public class ParametersUtil {
 
 	@SuppressWarnings("unchecked")
 	public static void addParameterToParametersBoolean(FhirContext theCtx, IBaseParameters theParameters, String theName, boolean theValue) {
-		IPrimitiveType<Boolean> value = (IPrimitiveType<Boolean>) theCtx.getElementDefinition("boolean").newInstance();
+		addParameterToParameters(theCtx, theParameters, theName, theCtx.getPrimitiveBoolean(theValue));
-		value.setValue(theValue);
-		addParameterToParameters(theCtx, theParameters, theName, value);
 	}
 
 	@SuppressWarnings("unchecked")
@@ -310,10 +305,7 @@ public class ParametersUtil {
 	}
 
 	public static void addPartBoolean(FhirContext theContext, IBase theParameter, String theName, Boolean theValue) {
-		IPrimitiveType<Boolean> value = (IPrimitiveType<Boolean>) theContext.getElementDefinition("boolean").newInstance();
+		addPart(theContext, theParameter, theName, theContext.getPrimitiveBoolean(theValue));
-		value.setValue(theValue);
-
-		addPart(theContext, theParameter, theName, value);
 	}
 
 	public static void addPartDecimal(FhirContext theContext, IBase theParameter, String theName, Double theValue) {

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2332-placeholder-valuset-skips-terminology-storage.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2332
+title: "All created placeholder resources now have a meta extension with the url http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder
+ and the value 'true'.  Also, terminology storage is now skipped for placeholder ValueSet and ConceptMap resources."

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java

@@ -88,7 +88,7 @@ public class DaoConfig {
 	 * Child Configurations
 	 */
 
-	private ModelConfig myModelConfig = new ModelConfig();
+	private final ModelConfig myModelConfig = new ModelConfig();
 
 	/**
 	 * update setter javadoc if default changes
@@ -171,7 +171,7 @@ public class DaoConfig {
 	 *
 	 * @since 4.1.0
 	 */
-	private int myPreExpandValueSetsDefaultOffset = 0;
+	private final int myPreExpandValueSetsDefaultOffset = 0;
 	/**
 	 * Do not change default of {@code 1000}!
 	 *
@@ -1067,6 +1067,9 @@ public class DaoConfig {
 	 * This property can be useful in cases where replication between two servers is wanted.
 	 * Note however that references containing purely numeric IDs will not be auto-created
 	 * as they are never allowed to be client supplied in HAPI FHIR JPA.
+	 *
+	 * All placeholder resources created in this way have a meta extension
+	 * with the URL {@link HapiExtensions#EXT_RESOURCE_META_PLACEHOLDER} and the value "true".
 	 * </p>
 	 */
 	public boolean isAutoCreatePlaceholderReferenceTargets() {
@@ -1088,6 +1091,9 @@ public class DaoConfig {
 	 * This property can be useful in cases where replication between two servers is wanted.
 	 * Note however that references containing purely numeric IDs will not be auto-created
 	 * as they are never allowed to be client supplied in HAPI FHIR JPA.
+	 *
+	 * All placeholder resources created in this way have a meta extension
+	 * with the URL {@link HapiExtensions#EXT_RESOURCE_META_PLACEHOLDER} and the value "true".
 	 * </p>
 	 */
 	public void setAutoCreatePlaceholderReferenceTargets(boolean theAutoCreatePlaceholderReferenceTargets) {

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

@@ -37,7 +37,11 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.HapiExtensions;
 import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
+import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -119,6 +123,13 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 			@SuppressWarnings("unchecked")
 			T newResource = (T) missingResourceDef.newInstance();
 
+			IBaseMetaType meta = newResource.getMeta();
+			if (meta instanceof IBaseHasExtensions) {
+				IBaseExtension<?, ?> extension = ((IBaseHasExtensions) meta).addExtension();
+				extension.setUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
+				extension.setValue(myContext.getPrimitiveBoolean(true));
+			}
+
 			IFhirResourceDao<T> placeholderResourceDao = myDaoRegistry.getResourceDao(theType);
 			ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
 

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

@@ -127,6 +127,7 @@ import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.IntegerType;
+import org.hl7.fhir.r4.model.MetadataResource;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
@@ -656,9 +657,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			return true;
 
 		//-- token case
-		if (startsWithByWordBoundaries(theDisplay, theFilterDisplay)) return true;
+		return startsWithByWordBoundaries(theDisplay, theFilterDisplay);
-
-		return false;
 	}
 
 	private boolean startsWithByWordBoundaries(String theDisplay, String theFilterDisplay) {
@@ -1770,10 +1769,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	@Override
 	@Transactional
 	public void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap) {
-		ourLog.debug("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
+		if (isPlaceholder(theConceptMap)) {
+			ourLog.info("Not storing TermConceptMap for placeholder {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
+			return;
+		}
+
 		ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theConceptMap.getUrl(), "ConceptMap has no value for ConceptMap.url");
+		ourLog.info("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
 
 		TermConceptMap termConceptMap = new TermConceptMap();
 		termConceptMap.setResource(theResourceTable);
@@ -2063,10 +2067,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	@Override
 	@Transactional
 	public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
-		ourLog.info("Storing TermValueSet for {}", theValueSet.getIdElement().toVersionless().getValueAsString());
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
+		if (isPlaceholder(theValueSet)) {
+			ourLog.info("Not storing TermValueSet for placeholder {}", theValueSet.getIdElement().toVersionless().getValueAsString());
+			return;
+		}
+
 		ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
+		ourLog.info("Storing TermValueSet for {}", theValueSet.getIdElement().toVersionless().getValueAsString());
 
 		/*
 		 * Get CodeSystem and validate CodeSystemVersion
@@ -2113,6 +2122,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		}
 	}
 
+	private boolean isPlaceholder(MetadataResource theResource) {
+		return theResource.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER) != null;
+	}
 
 	@Override
 	@Transactional

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3PhoneticSearchNoFtTest.java

@@ -4,12 +4,11 @@ import ca.uhn.fhir.context.phonetic.ApacheEncoder;
 import ca.uhn.fhir.context.phonetic.PhoneticEncoderEnum;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.util.HapiExtensions;
 import org.apache.commons.codec.language.Soundex;
-import org.aspectj.lang.annotation.Before;
 import org.hl7.fhir.dstu3.model.Enumerations;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.SearchParameter;
@@ -126,7 +125,7 @@ public class FhirResourceDaoDstu3PhoneticSearchNoFtTest extends BaseJpaDstu3Test
 //		searchParameter.setXpathUsage(SearchParameter.XPathUsageType.PHONETIC);
 		searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
 		searchParameter.addExtension()
-			.setUrl(JpaConstants.EXT_SEARCHPARAM_PHONETIC_ENCODER)
+			.setUrl(HapiExtensions.EXT_SEARCHPARAM_PHONETIC_ENCODER)
 			.setValue(new StringType(theEncoder.name()));
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
 		mySearchParameterDao.create(searchParameter, mySrd).getId().toUnqualifiedVersionless();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
 import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
 import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionResourceDao;
@@ -19,7 +20,6 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
-import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
@@ -48,6 +48,7 @@ import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Slice;
 
@@ -94,6 +95,9 @@ public class NpmR4Test extends BaseJpaR4Test {
 	private IInterceptorService myInterceptorService;
 	@Autowired
 	private RequestTenantPartitionInterceptor myRequestTenantPartitionInterceptor;
+	@Autowired
+	@Qualifier("myImplementationGuideDaoR4")
+	protected IFhirResourceDao<ImplementationGuide> myImplementationGuideDao;
 
 	@BeforeEach
 	public void before() throws Exception {
@@ -118,6 +122,7 @@ public class NpmR4Test extends BaseJpaR4Test {
 	public void after() throws Exception {
 		JettyUtil.closeServer(myServer);
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(new DaoConfig().isAutoCreatePlaceholderReferenceTargets());
 		myPartitionSettings.setPartitioningEnabled(false);
 		myInterceptorService.unregisterInterceptor(myRequestTenantPartitionInterceptor);
 	}
@@ -352,6 +357,34 @@ public class NpmR4Test extends BaseJpaR4Test {
 		}
 	}
 
+	// Reproduces https://github.com/hapifhir/hapi-fhir/issues/2332
+	@Test
+	public void testInstallR4Package_AutoCreatePlaceholder() throws Exception {
+		myDaoConfig.setAllowExternalReferences(true);
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+
+		byte[] bytes = loadClasspathBytes("/packages/test-auto-create-placeholder.tgz");
+		myFakeNpmServlet.myResponses.put("/test-ig/1.0.0", bytes);
+
+		List<String> resourceList = new ArrayList<>();
+		resourceList.add("ImplementationGuide");
+		PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-ig").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		spec.setInstallResourceTypes(resourceList);
+		PackageInstallOutcomeJson outcome = igInstaller.install(spec);
+		assertEquals(1, outcome.getResourcesInstalled().get("ImplementationGuide"));
+
+		// Be sure no further communication with the server
+		JettyUtil.closeServer(myServer);
+
+		// Search for the installed resources
+		runInTransaction(() -> {
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
+			IBundleProvider result = myImplementationGuideDao.search(map);
+			assertEquals(1, result.sizeOrThrowNpe());
+		});
+
+	}
+
 	@Test
 	public void testInstallR4Package_DraftResourcesNotInstalled() throws Exception {
 		myDaoConfig.setAllowExternalReferences(true);

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.model.util;
  */
 
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.util.HapiExtensions;
 
 public class JpaConstants {
 
@@ -195,9 +196,11 @@ public class JpaConstants {
 	public static final String EXTENSION_EXT_SYSTEMDEFINED = JpaConstants.class.getName() + "_EXTENSION_EXT_SYSTEMDEFINED";
 
 	/**
-	 * URL for extension on a Phonetic String SearchParameter indicating that text values should be phonetically indexed with the named encoder
+	 * Deprecated.  Please use {@link HapiExtensions#EXT_SEARCHPARAM_PHONETIC_ENCODER} instead.
 	 */
-	public static final String EXT_SEARCHPARAM_PHONETIC_ENCODER = "http://hapifhir.io/fhir/StructureDefinition/searchparameter-phonetic-encoder";
+	@Deprecated
+	public static final String EXT_SEARCHPARAM_PHONETIC_ENCODER = HapiExtensions.EXT_SEARCHPARAM_PHONETIC_ENCODER;
+
 	public static final String VALUESET_FILTER_DISPLAY = "display";
 
 	/**

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParameterCanonicalizer.java

@@ -23,7 +23,6 @@ package ca.uhn.fhir.jpa.searchparam.registry;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.phonetic.PhoneticEncoderEnum;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
@@ -431,7 +430,7 @@ public class SearchParameterCanonicalizer {
 				String nextUrl = next.getUrl();
 				if (isNotBlank(nextUrl)) {
 					theRuntimeSearchParam.addExtension(nextUrl, next);
-					if (JpaConstants.EXT_SEARCHPARAM_PHONETIC_ENCODER.equals(nextUrl)) {
+					if (HapiExtensions.EXT_SEARCHPARAM_PHONETIC_ENCODER.equals(nextUrl)) {
 						setEncoder(theRuntimeSearchParam, next.getValue());
 					}
 				}