Merge branch 'hapifhir:master' into feat/remote-terminology-support

.github/workflows/spotless-check.yml

@@ -22,6 +22,7 @@ jobs:
       -  uses: mshick/add-pr-comment@v2
          if: always()
          with:
+           proxy-url: https://slack-bots.azure.smilecdr.com/robogary/github
            message-success: |
              Formatting check succeeded!
            message-failure: |

pom.xml

@@ -6,6 +6,7 @@
     <properties>
         <java.version>17</java.version>
         <hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
+        <clinical-reasoning.version>3.20.0</clinical-reasoning.version>
     </properties>
 
     <!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
@@ -113,9 +114,9 @@
         </dependency>
         <!-- This dependency includes the JPA CQL Server -->
         <dependency>
-            <groupId>ca.uhn.hapi.fhir</groupId>
+            <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>hapi-fhir-storage-cr</artifactId>
+            <artifactId>cqf-fhir-cr-hapi</artifactId>
-            <version>${project.parent.version}</version>
+            <version>${clinical-reasoning.version}</version>
         </dependency>
         <!-- This dependency includes the JPA MDM Server -->
         <dependency>

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java

@@ -24,7 +24,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
 import java.io.IOException;
 import java.util.stream.Collectors;
 
-import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
+import static org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
 
 @Configurable
 public class CdsHooksServlet extends HttpServlet {

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java

@@ -5,14 +5,16 @@ import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
 import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
 import ca.uhn.fhir.jpa.starter.cr.CrProperties;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
-import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
 import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceRegistry;
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceRegistry;
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CdsCrDiscoveryServiceRegistry;
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICdsCrDiscoveryServiceRegistry;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrServiceRegistry;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrSettings;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.ICdsCrServiceRegistry;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.CdsCrDiscoveryServiceRegistry;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICdsCrDiscoveryServiceRegistry;
+import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.context.annotation.Bean;
@@ -22,27 +24,14 @@ import org.springframework.context.annotation.Import;
 
 @Configuration
 @Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
-@Import({CdsHooksConfig.class, CrCommonConfig.class})
+@Import({RepositoryConfig.class, TestCdsHooksConfig.class, CrCdsHooksConfig.class, CrCommonConfig.class})
 public class StarterCdsHooksConfig {
 
-	//	@Bean
-	//	CdsPrefetchSvc cdsPrefetchSvc(
-	//		CdsResolutionStrategySvc theCdsResolutionStrategySvc,
-	//		CdsPrefetchDaoSvc theResourcePrefetchDao,
-	//		CdsPrefetchFhirClientSvc theResourcePrefetchFhirClient,
-	//		ICdsHooksDaoAuthorizationSvc theCdsHooksDaoAuthorizationSvc) {
-	//		return new ModuleConfigurationPrefetchSvc(
-	//			theCdsResolutionStrategySvc,
-	//			theResourcePrefetchDao,
-	//			theResourcePrefetchFhirClient,
-	//			theCdsHooksDaoAuthorizationSvc);
-	//	}
-
 	@Bean
 	public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
 		CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
 		registry.unregister(FhirVersionEnum.R4);
-		registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryServiceR4.class);
+		registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryService.class);
 		return registry;
 	}
 
@@ -50,7 +39,7 @@ public class StarterCdsHooksConfig {
 	public ICdsCrServiceRegistry cdsCrServiceRegistry() {
 		CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
 		registry.unregister(FhirVersionEnum.R4);
-		registry.register(FhirVersionEnum.R4, UpdatedCdsCrServiceR4.class);
+		registry.register(FhirVersionEnum.R4, UpdatedCdsCrService.class);
 		return registry;
 	}
 

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrService.java

@@ -0,0 +1,44 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrService;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
+
+import static org.opencds.cqf.fhir.utility.Constants.APPLY_PARAMETER_DATA;
+
+public class UpdatedCdsCrService extends CdsCrService {
+	private final IAdapterFactory adapterFactory;
+
+	public UpdatedCdsCrService(
+			RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
+		super(theRequestDetails, theRepository, theCdsConfigService);
+		adapterFactory = IAdapterFactory.forFhirContext(theRepository.fhirContext());
+	}
+
+	@Override
+	public IBaseParameters encodeParams(CdsServiceRequestJson theJson) {
+		var parameters = adapterFactory.createParameters(super.encodeParams(theJson));
+		if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
+			parameters.addParameter(
+					"useServerData",
+					booleanTypeForVersion(parameters.fhirContext().getVersion().getVersion(), false));
+		}
+		return (IBaseParameters) parameters.get();
+	}
+
+	private IPrimitiveType<Boolean> booleanTypeForVersion(FhirVersionEnum fhirVersion, boolean value) {
+		return switch (fhirVersion) {
+			case DSTU2 -> new org.hl7.fhir.dstu2.model.BooleanType(value);
+			case DSTU3 -> new org.hl7.fhir.dstu3.model.BooleanType(value);
+			case R4 -> new org.hl7.fhir.r4.model.BooleanType(value);
+			case R5 -> new org.hl7.fhir.r5.model.BooleanType(value);
+			default -> throw new IllegalArgumentException("unknown or unsupported FHIR version");
+		};
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrServiceR4.java

@@ -1,28 +0,0 @@
-package ca.uhn.fhir.jpa.starter.cdshooks;
-
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
-import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
-import org.hl7.fhir.r4.model.BooleanType;
-import org.hl7.fhir.r4.model.Parameters;
-import org.opencds.cqf.fhir.api.Repository;
-
-import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA;
-import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
-
-public class UpdatedCdsCrServiceR4 extends CdsCrServiceR4 {
-	public UpdatedCdsCrServiceR4(
-			RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
-		super(theRequestDetails, theRepository, theCdsConfigService);
-	}
-
-	@Override
-	public Parameters encodeParams(CdsServiceRequestJson theJson) {
-		Parameters parameters = super.encodeParams(theJson);
-		if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
-			parameters.addParameter(part("useServerData", new BooleanType(false)));
-		}
-		return parameters;
-	}
-}

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryService.java

@@ -0,0 +1,12 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.CrDiscoveryService;
+
+public class UpdatedCrDiscoveryService extends CrDiscoveryService {
+	public UpdatedCrDiscoveryService(IIdType thePlanDefinitionId, Repository theRepository) {
+		super(thePlanDefinitionId, theRepository);
+		maxUriLength = 6000;
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryServiceR4.java

@@ -1,12 +0,0 @@
-package ca.uhn.fhir.jpa.starter.cdshooks;
-
-import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.opencds.cqf.fhir.api.Repository;
-
-public class UpdatedCrDiscoveryServiceR4 extends CrDiscoveryServiceR4 {
-	public UpdatedCrDiscoveryServiceR4(IIdType thePlanDefinitionId, Repository theRepository) {
-		super(thePlanDefinitionId, theRepository);
-		myMaxUriLength = 6000;
-	}
-}

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

@@ -156,8 +156,8 @@ public class FhirServerConfigCommon {
 
 		jpaStorageSettings.setPreExpandValueSets(appProperties.getPre_expand_value_sets());
 		jpaStorageSettings.setEnableTaskPreExpandValueSets(appProperties.getEnable_task_pre_expand_value_sets());
-		jpaStorageSettings.setPreExpandValueSetsDefaultCount(appProperties.getPre_expand_value_sets_default_count());
 		jpaStorageSettings.setPreExpandValueSetsMaxCount(appProperties.getPre_expand_value_sets_max_count());
+		jpaStorageSettings.setPreExpandValueSetsDefaultCount(appProperties.getPre_expand_value_sets_default_count());
 		jpaStorageSettings.setMaximumExpansionSize(appProperties.getMaximum_expansion_size());
 
 		jpaStorageSettings.setIndexMissingFields(

src/main/java/ca/uhn/fhir/jpa/starter/cr/CrCommonConfig.java

@@ -1,8 +1,5 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
-import ca.uhn.fhir.cr.common.CqlThreadFactory;
-import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
@@ -19,6 +16,9 @@ import org.opencds.cqf.cql.engine.runtime.Code;
 import org.opencds.cqf.fhir.cql.EvaluationSettings;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
+import org.opencds.cqf.fhir.cr.hapi.common.CodeCacheResourceChangeListener;
+import org.opencds.cqf.fhir.cr.hapi.common.CqlThreadFactory;
+import org.opencds.cqf.fhir.cr.hapi.common.ElmCacheResourceChangeListener;
 import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
 import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
 import org.opencds.cqf.fhir.utility.ValidationProfile;

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrDstu3Config.java

@@ -1,11 +1,11 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import ca.uhn.fhir.cr.config.dstu3.ApplyOperationConfig;
-import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
-import ca.uhn.fhir.cr.config.dstu3.DataRequirementsOperationConfig;
-import ca.uhn.fhir.cr.config.dstu3.EvaluateOperationConfig;
-import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
+import org.opencds.cqf.fhir.cr.hapi.config.dstu3.ApplyOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.dstu3.CrDstu3Config;
+import org.opencds.cqf.fhir.cr.hapi.config.dstu3.DataRequirementsOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.dstu3.EvaluateOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.dstu3.PackageOperationConfig;
 import org.springframework.context.annotation.*;
 
 @Configuration

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java

@@ -1,14 +1,14 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
-import ca.uhn.fhir.cr.config.r4.CrR4Config;
-import ca.uhn.fhir.cr.config.r4.DataRequirementsOperationConfig;
-import ca.uhn.fhir.cr.config.r4.EvaluateOperationConfig;
-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.r4.QuestionnaireOperationConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.ApplyOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.CrR4Config;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.DataRequirementsOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.EvaluateOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.ExtractOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.PackageOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.PopulateOperationConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.r4.QuestionnaireOperationConfig;
 import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;

src/main/resources/cds.application.yaml

@@ -124,7 +124,7 @@ hapi:
         data:
           search_parameter_mode: USE_SEARCH_PARAMETERS # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY
           terminology_parameter_mode: FILTER_IN_MEMORY #  AUTO, USE_VALUE_SET_URL, USE_INLINE_CODES, FILTER_IN_MEMORY
-          profile_mode: OFF # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
+          profile_mode: DECLARED # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
 
     cdshooks:
       enabled: true

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

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.cr.config.RepositoryConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
 import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
@@ -9,7 +8,6 @@ import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
-import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
 import com.google.gson.Gson;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonObject;
@@ -22,6 +20,9 @@ import org.apache.http.impl.client.HttpClients;
 import org.apache.http.util.EntityUtils;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
+import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.server.LocalServerPort;
@@ -39,7 +40,8 @@ import static org.junit.jupiter.api.Assertions.fail;
 		Application.class,
 		NicknameServiceConfig.class,
 		RepositoryConfig.class,
-		CdsHooksConfig.class,
+		TestCdsHooksConfig.class,
+		CrCdsHooksConfig.class,
 		StarterCdsHooksConfig.class
 	}, properties = {
 	"spring.profiles.include=storageSettingsTest",
@@ -116,7 +118,7 @@ class CdsHooksServletIT implements IServerSupport {
 	}
 
 	@Test
-	void testCdsHooks() throws IOException, InterruptedException {
+	void testCdsHooks() throws IOException {
 		loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
 		await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
 		var cdsRequest = "{\n" +

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.cr.config.RepositoryConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
@@ -19,6 +18,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.server.LocalServerPort;

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.cr.config.RepositoryConfig;
 import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
 import ca.uhn.fhir.jpa.starter.cr.CrProperties;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -25,6 +24,7 @@ import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
+import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.server.LocalServerPort;