Upgrade HAPI to 8.8

cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/config/CrCdsHooksConfig.java

@@ -1,7 +1,9 @@
 package org.opencds.cqf.fhir.cr.hapi.config;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.repository.IRepository;
 import ca.uhn.fhir.rest.api.server.IRepositoryFactory;
@@ -124,6 +126,7 @@ public CdsServiceInterceptor cdsServiceInterceptor(
             CdsServiceRegistryImpl cdsServiceRegistry,
             ICrDiscoveryServiceFactory discoveryServiceFactory,
             ICdsCrServiceFactory crServiceFactory,
+            PartitionSettings partitionSettings,
             Optional<IResourceChangeListenerRegistry> resourceChangeListenerRegistry) {
         if (resourceChangeListenerRegistry.isEmpty()) {
             return null;
@@ -132,7 +135,11 @@ public CdsServiceInterceptor cdsServiceInterceptor(
         resourceChangeListenerRegistry
                 .get()
                 .registerResourceResourceChangeListener(
-                        PLAN_DEFINITION_RESOURCE_NAME, SearchParameterMap.newSynchronous(), listener, 1000);
+                        PLAN_DEFINITION_RESOURCE_NAME,
+                        RequestPartitionId.defaultPartition(partitionSettings),
+                        SearchParameterMap.newSynchronous(),
+                        listener,
+                        1000);
         return listener;
     }
 }

cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/config/test/TestCrConfig.java

@@ -1,18 +1,21 @@
 package org.opencds.cqf.fhir.cr.hapi.config.test;
 
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
+import ca.uhn.fhir.batch2.jobs.bulkmodify.reindex.ReindexProvider;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerCacheRefresher;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheFactory;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheRefresherImpl;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryImpl;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.provider.DiffProvider;
 import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
@@ -26,6 +29,7 @@
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
+import jakarta.annotation.Nonnull;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
@@ -49,6 +53,9 @@
 @Configuration
 @Import({SubscriptionSubmitterConfig.class, SubscriptionChannelConfig.class})
 public class TestCrConfig {
+    public static final String LIBRARY_RESOURCE_NAME = "Library";
+    public static final String VALUESET_RESOURCE_NAME = "ValueSet";
+
     @Bean
     public RestfulServer restfulServer(
             IFhirSystemDao<?, ?> fhirSystemDao,
@@ -116,26 +123,28 @@ public Map<String, List<Code>> globalValueSetCache() {
     @Bean
     public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
             IResourceChangeListenerRegistry resourceChangeListenerRegistry,
+            PartitionSettings partitionSettings,
             DaoRegistry daoRegistry,
             EvaluationSettings evaluationSettings) {
         ElmCacheResourceChangeListener listener =
                 new ElmCacheResourceChangeListener(daoRegistry, evaluationSettings.getLibraryCache());
-        resourceChangeListenerRegistry.registerResourceResourceChangeListener(
-                "Library", SearchParameterMap.newSynchronous(), listener, 1000);
+        registerResourceResourceChangeListener(
+                resourceChangeListenerRegistry, partitionSettings, listener, LIBRARY_RESOURCE_NAME);
         return listener;
     }
 
     @Bean
     public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
             IResourceChangeListenerRegistry resourceChangeListenerRegistry,
             EvaluationSettings evaluationSettings,
+            PartitionSettings partitionSettings,
             DaoRegistry daoRegistry) {
 
         CodeCacheResourceChangeListener listener =
                 new CodeCacheResourceChangeListener(daoRegistry, evaluationSettings.getValueSetCache());
         // registry
-        resourceChangeListenerRegistry.registerResourceResourceChangeListener(
-                "ValueSet", SearchParameterMap.newSynchronous(), listener, 1000);
+        registerResourceResourceChangeListener(
+                resourceChangeListenerRegistry, partitionSettings, listener, VALUESET_RESOURCE_NAME);
 
         return listener;
     }
@@ -144,9 +153,10 @@ public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
     public IResourceChangeListenerRegistry resourceChangeListenerRegistry(
             InMemoryResourceMatcher inMemoryResourceMatcher,
             FhirContext fhirContext,
+            PartitionSettings partitionSettings,
             ResourceChangeListenerCacheFactory resourceChangeListenerCacheFactory) {
         return new ResourceChangeListenerRegistryImpl(
-                fhirContext, resourceChangeListenerCacheFactory, inMemoryResourceMatcher);
+                fhirContext, partitionSettings, resourceChangeListenerCacheFactory, inMemoryResourceMatcher);
     }
 
     @Bean
@@ -158,4 +168,28 @@ IResourceChangeListenerCacheRefresher resourceChangeListenerCacheRefresher() {
     public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
         return new ResourceChangeListenerRegistryInterceptor();
     }
+
+    @Bean
+    public PartitionSettings partitionSettings() {
+        return new PartitionSettings();
+    }
+
+    private void registerResourceResourceChangeListener(
+            IResourceChangeListenerRegistry resourceChangeListenerRegistry,
+            PartitionSettings partitionSettings,
+            IResourceChangeListener listener,
+            String resourceType) {
+
+        resourceChangeListenerRegistry.registerResourceResourceChangeListener(
+                resourceType,
+                getRequestPartitionId(partitionSettings),
+                SearchParameterMap.newSynchronous(),
+                listener,
+                1000);
+    }
+
+    @Nonnull
+    private RequestPartitionId getRequestPartitionId(PartitionSettings partitionSettings) {
+        return RequestPartitionId.defaultPartition(partitionSettings);
+    }
 }

cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/repository/ClinicalIntelligenceHapiFhirRepository.java

@@ -5,27 +5,30 @@
 import static java.util.Objects.nonNull;
 
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.repository.HapiFhirRepository;
-import ca.uhn.fhir.jpa.repository.SearchConverter;
-import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.jpa.repository.searchparam.SearchParameterMapRepositoryRestQueryBuilder;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.repository.impl.MultiMapRepositoryRestQueryBuilder;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.RestfulServerUtils;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
-import com.google.common.collect.Multimap;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -37,9 +40,10 @@
  * Since hapi-fhir is released quarterly, we want to maintain flexibility to change behaviour
  * within our more flexible release cadence.
  */
+@SuppressWarnings("UnstableApiUsage")
 public class ClinicalIntelligenceHapiFhirRepository extends HapiFhirRepository {
 
-    private static final Logger ourLog = LoggerFactory.getLogger(ClinicalIntelligenceHapiFhirRepository.class);
+    private static final Logger logger = LoggerFactory.getLogger(ClinicalIntelligenceHapiFhirRepository.class);
 
     private final RequestDetails requestDetails;
     private final RestfulServer restfulServer;
@@ -53,8 +57,17 @@ public ClinicalIntelligenceHapiFhirRepository(
         this.daoRegistry = daoRegistry;
     }
 
+    @Override
+    public <T extends IBaseResource, I extends IIdType> T read(
+            Class<T> resourceType, I id, Map<String, String> headers) {
+
+        return (T) this.daoRegistry
+                .getResourceDao(resourceType)
+                .read(id, cloneWithAction(resourceType, headers, RestOperationTypeEnum.READ));
+    }
+
     /**
-     * Override {@link HapiFhirRepository#search(Class, Class, Map, Map)} to ensure that the
+     * Override {@link HapiFhirRepository#search(Class, Class, IRepositoryRestQueryContributor, Map)} to ensure that the
      * _count {@link RequestDetails} parameter is passed through to the DAO layer instead of
      * dropping it.
      * <p/>
@@ -67,18 +80,15 @@ public ClinicalIntelligenceHapiFhirRepository(
     public <B extends IBaseBundle, T extends IBaseResource> B search(
             Class<B> bundleType,
             Class<T> resourceType,
-            Multimap<String, List<IQueryParameterType>> searchParameters,
+            IRepositoryRestQueryContributor queryContributor,
             Map<String, String> headers) {
 
-        var details = ClinicalIntelligenceRequestDetailsCloner.startWith(requestDetails)
-                .setAction(RestOperationTypeEnum.SEARCH_TYPE)
-                .addHeaders(headers)
-                .create();
+        var details = cloneWithAction(resourceType, headers, RestOperationTypeEnum.SEARCH_TYPE);
 
-        var converter = new SearchConverter();
-        converter.convertParameters(searchParameters, fhirContext());
-        details.setParameters(converter.myResultParameters);
+        var searchParameterMap =
+                SearchParameterMapRepositoryRestQueryBuilder.buildFromQueryContributor(queryContributor);
 
+        details.setParameters(MultiMapRepositoryRestQueryBuilder.toFlatMap(searchParameterMap));
         details.setResourceName(daoRegistry.getFhirContext().getResourceType(resourceType));
 
         if (details instanceof SystemRequestDetails) {
@@ -89,13 +99,55 @@ public <B extends IBaseBundle, T extends IBaseResource> B search(
         }
 
         var resourceDao = daoRegistry.getResourceDao(resourceType);
-        var bundleProvider = resourceDao.search(converter.mySearchParameterMap, details);
+        var bundleProvider = resourceDao.search(searchParameterMap, details);
 
         bundleProvider = sanitizeBundleProvider(bundleProvider);
 
         return createBundle(details, bundleProvider);
     }
 
+    public <T extends IBaseResource> MethodOutcome create(T resource, Map<String, String> headers) {
+        return this.daoRegistry
+                .getResourceDao(resource)
+                .create(resource, cloneWithAction(resource, headers, RestOperationTypeEnum.CREATE));
+    }
+
+    public <T extends IBaseResource> MethodOutcome update(T resource, Map<String, String> headers) {
+        final DaoMethodOutcome update = daoRegistry
+                .getResourceDao(resource)
+                .update(resource, cloneWithAction(resource, headers, RestOperationTypeEnum.UPDATE));
+        boolean created = update.getCreated() != null && update.getCreated();
+        if (created) {
+            update.setResponseStatusCode(201);
+        } else {
+            update.setResponseStatusCode(200);
+        }
+
+        return update;
+    }
+
+    public <I extends IIdType, P extends IBaseParameters> MethodOutcome patch(
+            I id, P patchParameters, Map<String, String> headers) {
+        return this.daoRegistry
+                .getResourceDao(id.getResourceType())
+                .patch(
+                        id,
+                        (String) null,
+                        PatchTypeEnum.FHIR_PATCH_JSON,
+                        (String) null,
+                        patchParameters,
+                        cloneWithAction(patchParameters, headers, RestOperationTypeEnum.PATCH));
+    }
+
+    public <T extends IBaseResource, I extends IIdType> MethodOutcome delete(
+            Class<T> resourceType, I id, Map<String, String> headers) {
+        return this.daoRegistry
+                .getResourceDao(resourceType)
+                .delete(id, cloneWithAction(resourceType, headers, RestOperationTypeEnum.DELETE));
+    }
+
+    // N.B. We don't support request details cloning for link
+
     protected IBundleProvider sanitizeBundleProvider(IBundleProvider bundleProvider) {
         return nonNull(bundleProvider) ? bundleProvider : new SimpleBundleProvider();
     }
@@ -125,7 +177,7 @@ protected BundleTypeEnum extractBundleTypeFromRequestParameters(Map<String, Stri
         bundleType = BundleTypeEnum.VALUESET_BINDER.fromCodeString(bundleTypeValues[0]);
 
         if (isNull(bundleType)) {
-            ourLog.error(
+            logger.error(
                     "Could not convert value {} to a BundleTypeEnum.  Defaulting to {}",
                     bundleTypeValues[0],
                     bundleType);
@@ -135,6 +187,21 @@ protected BundleTypeEnum extractBundleTypeFromRequestParameters(Map<String, Stri
         return bundleType;
     }
 
+    private <T extends IBaseResource> RequestDetails cloneWithAction(
+            T resource, Map<String, String> headers, RestOperationTypeEnum operationTypeEnum) {
+        return cloneWithAction(resource.getClass(), headers, operationTypeEnum);
+    }
+
+    private <T extends IBaseResource> RequestDetails cloneWithAction(
+            Class<T> resourceType, Map<String, String> headers, RestOperationTypeEnum operationTypeEnum) {
+
+        return ClinicalIntelligenceRequestDetailsCloner.startWith(
+                        requestDetails, daoRegistry.getFhirContext(), resourceType)
+                .setAction(operationTypeEnum)
+                .addHeaders(headers)
+                .create();
+    }
+
     private <B extends IBaseBundle> B createBundle(RequestDetails requestDetails, IBundleProvider bundleProvider) {
 
         Integer count = RestfulServerUtils.extractCountParameter(requestDetails);