Expose hapi-fhir-storage-cr config to downstream modules for testing (#6272)

* Ensure IRepositoryFactory returns a Repository, and not a HapiFhirRepository.

* Rename test so that it will run from Maven and the pipeline since it didn't before.  Fix small bug that made the test error out.

* Move TestCrConfig and TestCrR4Config to main source folder.  Extract TestHapiFhirCrPartitionConfig as separate test config to be used only in the test source folder.  Add Maven compile dependency to hapi-fhir-jpaserver-base in order to ensure that moved Config classes will compile.

* Add possible code change to RequestDetailsClone to clone partition info.

* Introduce separate factory interface for Repository to preserve backward compatibility.

* Remove IRepositoryFactoryForInterface.

* Spotless

* Add javadoc.

* Get rid of TODO.

* Restore RepositoryConfig to master.

* Move test config to different packages.

* Leverage use of new RepositoryFactoryForRepositoryInterface for CrR4Config and RepositoryFactoryForRepositoryInterface.

* Ensure CrR4Config and RepositoryConfig make use of new RepositoryFactoryForRepositoryInterface.

* Add copyright header

* Add @FunctionalInterface to factory.

hapi-fhir-storage-cr/pom.xml

@@ -145,6 +145,20 @@
 			<artifactId>jakarta.xml.bind-api</artifactId>
 		</dependency>
 
+		<!-- For test CR config that's exported to downstream modules -->
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-base</artifactId>
+			<version>${project.version}</version>
+			<exclusions>
+				<!-- prevent conflict with other version of this dependency sourced from elsewhere -->
+				<exclusion>
+					<groupId>org.glassfish</groupId>
+					<artifactId>jakarta.json</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+
 		<!-- test -->
 		<dependency>
 			<groupId>org.testcontainers</groupId>

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/IRepositoryFactory.java

@@ -21,8 +21,10 @@ package ca.uhn.fhir.cr.common;
 
 import ca.uhn.fhir.cr.repo.HapiFhirRepository;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import com.google.common.annotations.Beta;
 
 @FunctionalInterface
+@Beta
 public interface IRepositoryFactory {
 	HapiFhirRepository create(RequestDetails theRequestDetails);
 }

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/RepositoryFactoryForRepositoryInterface.java

@@ -0,0 +1,31 @@
+/*-
+ * #%L
+ * HAPI FHIR - Clinical Reasoning
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+package ca.uhn.fhir.cr.common;
+
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.opencds.cqf.fhir.api.Repository;
+
+/**
+ * Factory interface to return a {@link Repository} from a {@link RequestDetails}
+ */
+@FunctionalInterface
+public interface RepositoryFactoryForRepositoryInterface {
+	Repository create(RequestDetails theRequestDetails);
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/RepositoryConfig.java

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.cr.config;
 
 import ca.uhn.fhir.cr.common.IRepositoryFactory;
+import ca.uhn.fhir.cr.common.RepositoryFactoryForRepositoryInterface;
 import ca.uhn.fhir.cr.repo.HapiFhirRepository;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.rest.server.RestfulServer;
@@ -28,8 +29,15 @@ import org.springframework.context.annotation.Configuration;
 
 @Configuration
 public class RepositoryConfig {
+
 	@Bean
 	IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
 		return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
 	}
+
+	@Bean
+	RepositoryFactoryForRepositoryInterface repositoryFactoryForInterface(
+			DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
+		return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
+	}
 }

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/r4/CrR4Config.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.cr.config.r4;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.cr.common.IRepositoryFactory;
+import ca.uhn.fhir.cr.common.RepositoryFactoryForRepositoryInterface;
 import ca.uhn.fhir.cr.config.ProviderLoader;
 import ca.uhn.fhir.cr.config.ProviderSelector;
 import ca.uhn.fhir.cr.config.RepositoryConfig;
@@ -66,7 +67,8 @@ public class CrR4Config {
 
 	@Bean
 	IMeasureServiceFactory r4MeasureServiceFactory(
-			IRepositoryFactory theRepositoryFactory, MeasureEvaluationOptions theEvaluationOptions) {
+			RepositoryFactoryForRepositoryInterface theRepositoryFactory,
+			MeasureEvaluationOptions theEvaluationOptions) {
 		return rd -> new R4MeasureService(theRepositoryFactory.create(rd), theEvaluationOptions);
 	}
 

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/test/TestCqlProperties.java

@@ -1,4 +1,23 @@
-package ca.uhn.fhir.cr;
+/*-
+ * #%L
+ * HAPI FHIR - Clinical Reasoning
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+package ca.uhn.fhir.cr.config.test;
 
 import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
@@ -7,7 +26,9 @@ import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.opencds.cqf.fhir.cql.CqlEngineOptions;
 import org.opencds.cqf.fhir.cql.CqlOptions;
 
-
+/**
+ * Common CQL properties shared with downstream modules.
+ */
 public class TestCqlProperties {
 
 	//cql settings

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/test/TestCrConfig.java

@@ -1,4 +1,23 @@
-package ca.uhn.fhir.cr;
+/*-
+ * #%L
+ * HAPI FHIR - Clinical Reasoning
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+package ca.uhn.fhir.cr.config.test;
 
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
 import ca.uhn.fhir.context.FhirContext;
@@ -47,6 +66,9 @@ import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 
 
+/**
+ * Common hapi-fhir clinical reasoning config shared with downstream modules.
+ */
 @Configuration
 @Import({SubscriptionSubmitterConfig.class, SubscriptionChannelConfig.class})
 public class TestCrConfig {
@@ -77,7 +99,9 @@ public class TestCrConfig {
 	}
 	@Bean
 	public TestCqlProperties testCqlProperties(){
-		return new TestCqlProperties();}
+		return new TestCqlProperties();
+	}
+
 	@Bean
 	public JpaStorageSettings storageSettings() {
 		JpaStorageSettings storageSettings = new JpaStorageSettings();
@@ -87,12 +111,6 @@ public class TestCrConfig {
 		storageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
 		return storageSettings;
 	}
-
-	@Bean
-	public PartitionHelper partitionHelper() {
-		return new PartitionHelper();
-	}
-
 	@Bean
 	public ModelManager modelManager(Map<ModelIdentifier, Model> theGlobalModelCache) {
 		return new ModelManager(theGlobalModelCache);

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/test/r4/TestCrR4Config.java

@@ -1,9 +1,28 @@
-package ca.uhn.fhir.cr.r4;
+/*-
+ * #%L
+ * HAPI FHIR - Clinical Reasoning
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+package ca.uhn.fhir.cr.config.test.r4;
 
-import ca.uhn.fhir.cr.TestCqlProperties;
-import ca.uhn.fhir.cr.TestCrConfig;
 import ca.uhn.fhir.cr.common.CqlThreadFactory;
 import ca.uhn.fhir.cr.config.r4.CrR4Config;
+import ca.uhn.fhir.cr.config.test.TestCqlProperties;
+import ca.uhn.fhir.cr.config.test.TestCrConfig;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
 import org.cqframework.cql.cql2elm.model.Model;
@@ -30,6 +49,9 @@ import java.util.Set;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 
+/**
+ * Common hapi-fhir clinical reasoning config specifically for R4 shared with downstream modules.
+ */
 @Configuration
 @Import({TestCrConfig.class, CrR4Config.class})
 public class TestCrR4Config {

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/TestHapiFhirCrPartitionConfig.java

@@ -0,0 +1,10 @@
+package ca.uhn.fhir.cr;
+
+import org.springframework.context.annotation.Bean;
+
+public class TestHapiFhirCrPartitionConfig {
+	@Bean
+	public PartitionHelper partitionHelper() {
+		return new PartitionHelper();
+	}
+}

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/dstu3/TestCrDstu3Config.java

@@ -1,8 +1,9 @@
 package ca.uhn.fhir.cr.dstu3;
 
-import ca.uhn.fhir.cr.TestCqlProperties;
-import ca.uhn.fhir.cr.TestCrConfig;
+import ca.uhn.fhir.cr.TestHapiFhirCrPartitionConfig;
+import ca.uhn.fhir.cr.config.test.TestCqlProperties;
 import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
+import ca.uhn.fhir.cr.config.test.TestCrConfig;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
 import org.cqframework.cql.cql2elm.model.Model;
@@ -26,6 +27,7 @@ import java.util.Set;
 
 @Configuration
 @Import({
+	TestHapiFhirCrPartitionConfig.class,
 	TestCrConfig.class,
 	CrDstu3Config.class
 })

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/BaseCrR4TestServer.java

@@ -2,10 +2,12 @@ package ca.uhn.fhir.cr.r4;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.cr.IResourceLoader;
+import ca.uhn.fhir.cr.TestHapiFhirCrPartitionConfig;
 import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
 import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
 import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
 import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
+import ca.uhn.fhir.cr.config.test.r4.TestCrR4Config;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
@@ -38,6 +40,7 @@ import java.util.concurrent.TimeUnit;
 
 
 @ContextConfiguration(classes = {
+	TestHapiFhirCrPartitionConfig.class,
 	TestCrR4Config.class,
 	ApplyOperationConfig.class,
 	ExtractOperationConfig.class,