fixes for support of R4B / 6.2.0 (#455)

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>6.2.0-PRE18-SNAPSHOT</version>
+        <version>6.2.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -316,11 +316,18 @@
             <version>${spring_boot_version}</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-core -->
+        <dependency>
+            <groupId>io.micrometer</groupId>
+            <artifactId>micrometer-core</artifactId>
+            <version>1.9.4</version>
+        </dependency>
+
         <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
         <dependency>
             <groupId>io.micrometer</groupId>
             <artifactId>micrometer-registry-prometheus</artifactId>
-            <version>1.8.5</version>
+            <version>1.9.4</version>
         </dependency>
 
         <dependency>

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java

@@ -28,6 +28,10 @@ public class OnEitherVersion extends AnyNestedCondition {
   static class OnR4 {
   }
 
+	@Conditional(OnR4BCondition.class)
+	static class OnR4B {
+	}
+
   @Conditional(OnR5Condition.class)
   static class OnR5 {
   }

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4BCondition.java

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.jpa.starter.annotations;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class OnR4BCondition implements Condition {
+	@Override
+	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+		String version = conditionContext.
+			getEnvironment()
+			.getProperty("hapi.fhir.fhir_version")
+			.toUpperCase();
+
+		return FhirVersionEnum.R4B.name().equals(version);
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4B.java

@@ -0,0 +1,17 @@
+package ca.uhn.fhir.jpa.starter.common;
+
+import ca.uhn.fhir.jpa.config.r4b.JpaR4BConfig;
+import ca.uhn.fhir.jpa.starter.annotations.OnR4BCondition;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+@Configuration
+@Conditional(OnR4BCondition.class)
+@Import({
+	JpaR4BConfig.class,
+	StarterJpaConfig.class,
+	ElasticsearchConfig.class
+})
+public class FhirServerConfigR4B {
+}

src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java

@@ -26,7 +26,6 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
 import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
 import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
-import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
@@ -423,7 +422,6 @@ public class StarterJpaConfig {
 	public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, DaoConfig daoConfig, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
 		FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
 		if (fhirVersion == FhirVersionEnum.DSTU2) {
-
 			JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, daoConfig);
 			confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
 			return confProvider;
@@ -437,6 +435,11 @@ public class StarterJpaConfig {
 			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);
 			confProvider.setImplementationDescription("HAPI FHIR R4 Server");
 			return confProvider;
+		} else if (fhirVersion == FhirVersionEnum.R4B) {
+
+			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);
+			confProvider.setImplementationDescription("HAPI FHIR R4B Server");
+			return confProvider;
 		} else if (fhirVersion == FhirVersionEnum.R5) {
 
 			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);

src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4B.java

@@ -0,0 +1,77 @@
+package ca.uhn.fhir.jpa.starter.common.validation;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.interceptor.validation.IRepositoryValidatingRule;
+import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
+import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.starter.annotations.OnR4BCondition;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.TokenParam;
+import org.hl7.fhir.r4b.model.StructureDefinition;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
+
+/**
+ * This class can be customized to enable the {@link RepositoryValidatingInterceptor}
+ * on this server.
+ * <p>
+ * The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
+ * in order to use this class.
+ */
+@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
+@Configuration
+@Conditional(OnR4BCondition.class)
+public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryValidationInterceptorFactory {
+
+	private final FhirContext fhirContext;
+	private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
+	private final IFhirResourceDao structureDefinitionResourceProvider;
+
+	public RepositoryValidationInterceptorFactoryR4B(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
+		this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
+		this.fhirContext = daoRegistry.getSystemDao().getContext();
+		structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
+
+	}
+
+	@Override
+	public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
+
+		IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
+		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
+			.stream()
+			.map(StructureDefinition.class::cast)
+			.collect(Collectors.groupingBy(StructureDefinition::getType));
+
+		structureDefintions.forEach((key, value) -> {
+			String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
+			repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
+		});
+
+		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
+		return new RepositoryValidatingInterceptor(fhirContext, rules);
+	}
+
+	@Override
+	public RepositoryValidatingInterceptor build() {
+
+		// Customize the ruleBuilder here to have the rules you want! We will give a simple example
+		// of enabling validation for all Patient resources
+		repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
+
+		// Do not customize below this line
+		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
+		return new RepositoryValidatingInterceptor(fhirContext, rules);
+	}
+
+}

src/main/resources/application.yaml

@@ -48,8 +48,8 @@ spring:
 #      hibernate.search.backend.directory.root: target/lucenefiles
 #      hibernate.search.backend.lucene_version: lucene_current
   ### elastic parameters ===> see also elasticsearch section below <===
-      hibernate.search.backend.type: elasticsearch
+#      hibernate.search.backend.type: elasticsearch
-      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
 hapi:
   fhir:
     ### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java

@@ -0,0 +1,120 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4b.model.Bundle;
+import org.hl7.fhir.r4b.model.Patient;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Order;
+import org.junit.jupiter.api.Test;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.web.server.LocalServerPort;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = {
+	"spring.datasource.url=jdbc:h2:mem:dbr4b",
+	"hapi.fhir.enable_repository_validating_interceptor=true",
+	"hapi.fhir.fhir_version=r4b",
+	"hapi.fhir.subscription.websocket_enabled=false",
+	"hapi.fhir.mdm_enabled=false",
+	"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
+	"hapi.fhir.implementationguides.dk-core.version=1.1.0",
+	// Override is currently required when using MDM as the construction of the MDM
+	// beans are ambiguous as they are constructed multiple places. This is evident
+	// when running in a spring boot environment
+	"spring.main.allow-bean-definition-overriding=true"})
+class ExampleServerR4BIT {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4BIT.class);
+	private IGenericClient ourClient;
+	private FhirContext ourCtx;
+
+	@LocalServerPort
+	private int port;
+
+	@Test
+	@Order(0)
+	void testCreateAndRead() {
+		String methodName = "testCreateAndRead";
+		ourLog.info("Entering " + methodName + "()...");
+
+		Patient pt = new Patient();
+		pt.setActive(true);
+		pt.getBirthDateElement().setValueAsString("2020-01-01");
+		pt.addIdentifier().setSystem("http://foo").setValue("12345");
+		pt.addName().setFamily(methodName);
+		IIdType id = ourClient.create().resource(pt).execute().getId();
+
+		Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
+		assertEquals(methodName, pt2.getName().get(0).getFamily());
+
+	}
+
+
+	@Test
+	public void testBatchPutWithIdenticalTags() {
+		String batchPuts = "{\n" +
+			"\t\"resourceType\": \"Bundle\",\n" +
+			"\t\"id\": \"patients\",\n" +
+			"\t\"type\": \"batch\",\n" +
+			"\t\"entry\": [\n" +
+			"\t\t{\n" +
+			"\t\t\t\"request\": {\n" +
+			"\t\t\t\t\"method\": \"PUT\",\n" +
+			"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"resource\": {\n" +
+			"\t\t\t\t\"resourceType\": \"Patient\",\n" +
+			"\t\t\t\t\"id\": \"pat-1\",\n" +
+			"\t\t\t\t\"meta\": {\n" +
+			"\t\t\t\t\t\"tag\": [\n" +
+			"\t\t\t\t\t\t{\n" +
+			"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
+			"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
+			"\t\t\t\t\t\t}\n" +
+			"\t\t\t\t\t]\n" +
+			"\t\t\t\t}\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
+			"\t\t},\n" +
+			"\t\t{\n" +
+			"\t\t\t\"request\": {\n" +
+			"\t\t\t\t\"method\": \"PUT\",\n" +
+			"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"resource\": {\n" +
+			"\t\t\t\t\"resourceType\": \"Patient\",\n" +
+			"\t\t\t\t\"id\": \"pat-2\",\n" +
+			"\t\t\t\t\"meta\": {\n" +
+			"\t\t\t\t\t\"tag\": [\n" +
+			"\t\t\t\t\t\t{\n" +
+			"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
+			"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
+			"\t\t\t\t\t\t}\n" +
+			"\t\t\t\t\t]\n" +
+			"\t\t\t\t}\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
+			"\t\t}\n" +
+			"\t]\n" +
+			"}";
+		Bundle bundle = FhirContext.forR4B().newJsonParser().parseResource(Bundle.class, batchPuts);
+		ourClient.transaction().withBundle(bundle).execute();
+	}
+
+
+
+	@BeforeEach
+	void beforeEach() {
+
+		ourCtx = FhirContext.forR4B();
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+		String ourServerBase = "http://localhost:" + port + "/fhir/";
+		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+
+
+	}
+}