Merge remote-tracking branch 'origin/master' into rel_8_1_tracking

README.md

@@ -357,11 +357,10 @@ It is recommended to deploy a case-sensitive database prior to running HAPI FHIR
 Custom interceptors can be registered with the server by including the property `hapi.fhir.custom-interceptor-classes`. This will take a comma separated list of fully-qualified class names which will be registered with the server.
 Interceptors will be discovered in one of two ways:
 
-1) discovered from the Spring application context as existing Beans (can be used in conjunction with `hapi.fhir.custom-bean-packages`) or registered with Spring via other methods
+1) From the Spring application context as existing Beans (can be used in conjunction with `hapi.fhir.custom-bean-packages`) or registered with Spring via other methods
+2) Classes will be instantiated via reflection if no matching Bean is found
 
-or
+Interceptors can also be registered manually through `RestfulServer.registerInterceptor`. Take note that any interceptor registered in this way _will not fire_ for non-REST operations, e.g. creation through a DAO. To trigger in this case, you need to register your interceptors on the `IInterceptorService` bean.
-
-2) classes will be instantiated via reflection if no matching Bean is found
 
 ## Adding custom operations(providers)
 Custom operations(providers) can be registered with the server by including the property `hapi.fhir.custom-provider-classes`. This will take a comma separated list of fully-qualified class names which will be registered with the server.

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -106,6 +106,8 @@ public class AppProperties {
 	private Integer pre_expand_value_sets_max_count = 1000;
 	private Integer maximum_expansion_size = 1000;
 
+	private Map<String, RemoteSystem> remote_terminology_service = null;
+
 	public List<String> getCustomInterceptorClasses() {
 		return custom_interceptor_classes;
 	}
@@ -723,6 +725,14 @@ public class AppProperties {
 		this.maximum_expansion_size = maximum_expansion_size;
 	}
 
+	public Map<String, RemoteSystem> getRemoteTerminologyServicesMap() {
+		return remote_terminology_service;
+	}
+
+	public void setRemote_terminology_service(Map<String, RemoteSystem> remote_terminology_service) {
+		this.remote_terminology_service = remote_terminology_service;
+	}
+
 	public static class Cors {
 		private Boolean allow_Credentials = true;
 		private List<String> allowed_origin = List.of("*");
@@ -919,6 +929,27 @@ public class AppProperties {
 		}
 	}
 
+	public static class RemoteSystem {
+		private String system;
+		private String url;
+
+		public String getSystem() {
+			return system;
+		}
+
+		public void setSystem(String system) {
+			this.system = system;
+		}
+
+		public String getUrl() {
+			return url;
+		}
+
+		public void setUrl(String url) {
+			this.url = url;
+		}
+	}
+
 	public static class Subscription {
 
 		private Boolean resthook_enabled = false;

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

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.jpa.starter.common.validation;
+
+import ca.uhn.fhir.jpa.starter.AppProperties;
+import org.springframework.boot.context.properties.bind.Binder;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class OnRemoteTerminologyPresent implements Condition {
+	@Override
+	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+
+		AppProperties config = Binder.get(conditionContext.getEnvironment())
+				.bind("hapi.fhir", AppProperties.class)
+				.orElse(null);
+		if (config == null) return false;
+		if (config.getRemoteTerminologyServicesMap() == null) return false;
+		return !config.getRemoteTerminologyServicesMap().isEmpty();
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/terminology/TerminologyConfig.java

@@ -0,0 +1,68 @@
+package ca.uhn.fhir.jpa.starter.terminology;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.ConceptValidationOptions;
+import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValidationSupportContext;
+import ca.uhn.fhir.jpa.starter.AppProperties;
+import ca.uhn.fhir.jpa.starter.common.StarterJpaConfig;
+import ca.uhn.fhir.jpa.starter.common.validation.OnRemoteTerminologyPresent;
+import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+@Configuration
+@Conditional(OnRemoteTerminologyPresent.class)
+@Import(StarterJpaConfig.class)
+public class TerminologyConfig {
+
+	@Bean(name = "myHybridRemoteValidationSupportChain")
+	public IValidationSupport addRemoteValidation(
+			ValidationSupportChain theValidationSupport, FhirContext theFhirContext, AppProperties theAppProperties) {
+		var values = theAppProperties.getRemoteTerminologyServicesMap().values();
+
+		// If the remote terminology service is "*" and is the only one then forward all requests to the remote
+		// terminology service
+		if (values.size() == 1 && "*".equalsIgnoreCase(values.iterator().next().getSystem())) {
+			var remoteSystem = values.iterator().next();
+			theValidationSupport.addValidationSupport(
+					0, new RemoteTerminologyServiceValidationSupport(theFhirContext, remoteSystem.getUrl()));
+			return theValidationSupport;
+
+			// If there are multiple remote terminology services, then add each one to the validation chain
+		} else {
+			values.forEach((remoteSystem) -> theValidationSupport.addValidationSupport(
+					0, new RemoteTerminologyServiceValidationSupport(theFhirContext, remoteSystem.getUrl()) {
+						@Override
+						public boolean isCodeSystemSupported(
+								ValidationSupportContext theValidationSupportContext, String theSystem) {
+							return remoteSystem.getSystem().equalsIgnoreCase(theSystem);
+						}
+
+						@Override
+						public CodeValidationResult validateCode(
+								ValidationSupportContext theValidationSupportContext,
+								ConceptValidationOptions theOptions,
+								String theCodeSystem,
+								String theCode,
+								String theDisplay,
+								String theValueSetUrl) {
+							if (remoteSystem.getSystem().equalsIgnoreCase(theCodeSystem)) {
+								return super.validateCode(
+										theValidationSupportContext,
+										theOptions,
+										theCodeSystem,
+										theCode,
+										theDisplay,
+										theValueSetUrl);
+							}
+							return null;
+						}
+					}));
+		}
+		return theValidationSupport;
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java

@@ -40,6 +40,19 @@ public class EnvironmentHelper {
 			properties.put(strippedKey, entry.getValue().toString());
 		}
 
+		// also check for JPA properties set as environment variables, this is slightly hacky and doesn't cover all
+		// the naming conventions Springboot allows
+		// but there doesn't seem to be a better/deterministic way to get these properties when they are set as ENV
+		// variables and this at least provides
+		// a way to set them (in a docker container, for instance)
+		Map<String, Object> jpaPropsEnv = getPropertiesStartingWith(environment, "SPRING_JPA_PROPERTIES");
+		for (Map.Entry<String, Object> entry : jpaPropsEnv.entrySet()) {
+			String strippedKey = entry.getKey().replace("SPRING_JPA_PROPERTIES_", "");
+			strippedKey = strippedKey.replaceAll("_", ".");
+			strippedKey = strippedKey.toLowerCase();
+			properties.put(strippedKey, entry.getValue().toString());
+		}
+
 		// Spring Boot Autoconfiguration defaults
 		properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner");
 		properties.putIfAbsent(

src/main/resources/application.yaml

@@ -293,6 +293,18 @@ hapi:
     #    max_page_size: 200
     #    retain_cached_searches_mins: 60
     #    reuse_cached_search_results_millis: 60000
+    # The remote_terminology_service block is commented out by default because it requires external terminology service endpoints.
+    # Uncomment and configure the block below if you need to enable remote terminology validation or mapping.
+    #remote_terminology_service:
+    #  all:
+    #    system: '*'
+    #    url: 'https://tx.fhir.org/r4/'
+    #  snomed:
+    #    system: 'http://snomed.info/sct'
+    #    url: 'https://tx.fhir.org/r4/'
+    #  loinc:
+    #    system: 'http://loinc.org'
+    #    url: 'https://hapi.fhir.org/baseR4/'
     tester:
       home:
         name: Local Tester

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

@@ -18,17 +18,7 @@ import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.DateType;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Measure;
-import org.hl7.fhir.r4.model.MeasureReport;
-import org.hl7.fhir.r4.model.Observation;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Period;
-import org.hl7.fhir.r4.model.StringType;
-import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
@@ -74,10 +64,14 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
 	"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
 	"hapi.fhir.implementationguides.dk-core.version=1.1.0",
 	"hapi.fhir.auto_create_placeholder_reference_targets=true",
+	"hibernate.search.enabled=true",
 	// 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"})
+	"spring.main.allow-bean-definition-overriding=true",
+	"hapi.fhir.remote_terminology_service.snomed.system=http://snomed.info/sct",
+	"hapi.fhir.remote_terminology_service.snomed.url=https://tx.fhir.org/r4"
+})
 class ExampleServerR4IT implements IServerSupport {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
 	private IGenericClient ourClient;
@@ -358,6 +352,21 @@ class ExampleServerR4IT implements IServerSupport {
 		assertTrue(foundDobChange);
 	}
 
+	@Test
+	void testValidateRemoteTerminology() {
+
+		String testCodeSystem = "http://foo/cs";
+		String testValueSet = "http://foo/vs";
+		ourClient.create().resource(new CodeSystem().setUrl(testCodeSystem).addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("yes")).addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("no"))).execute();
+		ourClient.create().resource(new ValueSet().setUrl(testValueSet).setCompose(new ValueSet.ValueSetComposeComponent().addInclude(new ValueSet.ConceptSetComponent().setSystem(testValueSet)))).execute();
+
+		Parameters remoteResult = ourClient.operation().onType(ValueSet.class).named("$validate-code").withParameter(Parameters.class, "code", new StringType("22298006")).andParameter("system", new UriType("http://snomed.info/sct")).execute();
+		assertEquals(true, ((BooleanType) remoteResult.getParameterValue("result")).getValue());
+		assertEquals("Myocardial infarction", ((StringType) remoteResult.getParameterValue("display")).getValue());
+
+		Parameters localResult = ourClient.operation().onType(CodeSystem.class).named("$validate-code").withParameter(Parameters.class, "url", new UrlType(testCodeSystem)).andParameter("coding", new Coding(testCodeSystem, "yes", null)).execute();
+	}
+
 	@BeforeEach
 	void beforeEach() {
 

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java

@@ -11,12 +11,7 @@ import jakarta.websocket.ContainerProvider;
 import jakarta.websocket.Session;
 import jakarta.websocket.WebSocketContainer;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r5.model.Bundle;
+import org.hl7.fhir.r5.model.*;
-import org.hl7.fhir.r5.model.Enumerations;
-import org.hl7.fhir.r5.model.Observation;
-import org.hl7.fhir.r5.model.Patient;
-import org.hl7.fhir.r5.model.Subscription;
-import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -36,7 +31,9 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
      "spring.datasource.url=jdbc:h2:mem:dbr5",
      "hapi.fhir.fhir_version=r5",
 	  "hapi.fhir.cr_enabled=false",
-	  "hapi.fhir.subscription.websocket_enabled=true"
+	  "hapi.fhir.subscription.websocket_enabled=true",
+	  "hapi.fhir.remote_terminology_service.snomed.system=http://snomed.info/sct",
+	  "hapi.fhir.remote_terminology_service.snomed.url=https://tx.fhir.org/r5"
   })
 public class ExampleServerR5IT {
 
@@ -156,6 +153,22 @@ public class ExampleServerR5IT {
     ourClient.delete().resourceById(mySubscriptionId).execute();
   }
 
+
+	@Test
+	void testValidateRemoteTerminology() {
+
+		String testCodeSystem = "http://foo/cs";
+		String testValueSet = "http://foo/vs";
+		ourClient.create().resource(new CodeSystem().setUrl(testCodeSystem).addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("yes")).addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("no"))).execute();
+		ourClient.create().resource(new ValueSet().setUrl(testValueSet).setCompose(new ValueSet.ValueSetComposeComponent().addInclude(new ValueSet.ConceptSetComponent().setSystem(testValueSet)))).execute();
+
+		Parameters remoteResult = ourClient.operation().onType(ValueSet.class).named("$validate-code").withParameter(Parameters.class, "code", new StringType("22298006")).andParameter("system", new UriType("http://snomed.info/sct")).execute();
+		assertEquals(true, ((BooleanType) remoteResult.getParameterValue("result")).getValue());
+		assertEquals("Myocardial infarction", ((StringType) remoteResult.getParameterValue("display")).getValue());
+
+		Parameters localResult = ourClient.operation().onType(CodeSystem.class).named("$validate-code").withParameter(Parameters.class, "url", new UrlType(testCodeSystem)).andParameter("coding", new Coding(testCodeSystem, "yes", null)).execute();
+	}
+
   @BeforeEach
   void beforeEach() {
 

src/test/smoketest/plain_server.http

@@ -206,6 +206,7 @@ GET http://{{host}}/fhir/Patient/{{batch_patient_id}}/$everything
 
 ### Extended Operations - validate
 # https://hapifhir.io/hapi-fhir/docs/server_plain/rest_operations_operations.html
+# @timeout 180   # wait up to 2 minutes for the validate response
 POST http://{{host}}/fhir/Patient/{{batch_patient_id}}/$validate
 
 > {%