Fix openapi for R5 (#5115)

* Fix openapi for R5

* Add changelog

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5115-fix-openapi-for-r5.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 5115
+title: "OpenAPI definitions were not working for R5 JPA servers. This has been corrected."

hapi-fhir-server-openapi/pom.xml

@@ -71,6 +71,12 @@
 			<version>${project.version}</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-r5</artifactId>
+			<version>${project.version}</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>

hapi-fhir-server-openapi/src/main/java/ca/uhn/fhir/rest/openapi/OpenApiInterceptor.java

@@ -908,12 +908,14 @@ public class OpenApiInterceptor {
 						break;
 					case "Resource":
 						if (theResourceType != null) {
+							if (FHIR_CONTEXT_CANONICAL.getResourceTypes().contains(theResourceType)) {
 								IBaseResource resource = FHIR_CONTEXT_CANONICAL
 										.getResourceDefinition(theResourceType)
 										.newInstance();
 								resource.setId("1");
 								param.setResource((Resource) resource);
 							}
+						}
 						break;
 				}
 			}
@@ -1002,7 +1004,7 @@ public class OpenApiInterceptor {
 		}
 		return () -> {
 			IBaseResource example = null;
-			if (theResourceType != null) {
+			if (theResourceType != null && theFhirContext.getResourceTypes().contains(theResourceType)) {
 				example = theFhirContext.getResourceDefinition(theResourceType).newInstance();
 			}
 			return example;

hapi-fhir-server-openapi/src/test/java/ca/uhn/fhir/rest/openapi/OpenApiInterceptorTest.java

@@ -4,20 +4,19 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.Hook;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.Operation;
-import ca.uhn.fhir.rest.annotation.OperationParam;
-import ca.uhn.fhir.rest.annotation.Patch;
-import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.*;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
+import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.provider.HashMapResourceProvider;
+import ca.uhn.fhir.rest.server.provider.ServerCapabilityStatementProvider;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.test.utilities.HtmlUtil;
+import ca.uhn.fhir.test.utilities.HttpClientExtension;
 import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
 import ca.uhn.fhir.util.ExtensionConstants;
 import com.gargoylesoftware.htmlunit.html.DomElement;
@@ -30,24 +29,10 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
 import org.hamcrest.Matchers;
-import org.hl7.fhir.instance.model.api.IBaseBundle;
-import org.hl7.fhir.instance.model.api.IBaseCoding;
-import org.hl7.fhir.instance.model.api.IBaseConformance;
-import org.hl7.fhir.instance.model.api.IBaseParameters;
-import org.hl7.fhir.instance.model.api.IBaseReference;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.CapabilityStatement;
-import org.hl7.fhir.r4.model.DecimalType;
-import org.hl7.fhir.r4.model.Observation;
-import org.hl7.fhir.r4.model.Patient;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Order;
-import org.junit.jupiter.api.Test;
+import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.r5.model.ActorDefinition;
+import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.RegisterExtension;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -56,42 +41,95 @@ import javax.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
+import java.util.*;
 
 import static org.hamcrest.CoreMatchers.not;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.*;
 
 public class OpenApiInterceptorTest {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(OpenApiInterceptorTest.class);
-	private final FhirContext myFhirContext = FhirContext.forR4Cached();
-	@RegisterExtension
-	@Order(0)
-	protected RestfulServerExtension myServer = new RestfulServerExtension(myFhirContext)
-		.withServletPath("/fhir/*")
-		.withServer(t -> t.registerProvider(new HashMapResourceProvider<>(myFhirContext, Patient.class)))
-		.withServer(t -> t.registerProvider(new HashMapResourceProvider<>(myFhirContext, Observation.class)))
-		.withServer(t -> t.registerProvider(new MyLastNProvider()))
-		.withServer(t -> t.registerInterceptor(new ResponseHighlighterInterceptor()));
-	private CloseableHttpClient myClient;
+
+	@Nested
+	class R4 extends BaseOpenApiInterceptorTest {
+
+		@Override
+		FhirContext getContext() {
+			return FhirContext.forR4Cached();
+		}
+
+		@Test
+		public void testSwaggerUiWithResourceCounts() throws IOException {
+			myServer.getRestfulServer().registerInterceptor(new AddResourceCountsInterceptor());
+			myServer.getRestfulServer().registerInterceptor(new OpenApiInterceptor());
+
+			String url = "http://localhost:" + myServer.getPort() + "/fhir/swagger-ui/";
+			String resp = fetchSwaggerUi(url);
+			List<String> buttonTexts = parsePageButtonTexts(resp, url);
+			assertThat(buttonTexts.toString(), buttonTexts, Matchers.contains("All", "System Level Operations", "Patient 2", "OperationDefinition 1", "Observation 0"));
+		}
+
+		@Test
+		public void testSwaggerUiWithResourceCounts_OneResourceOnly() throws IOException {
+			myServer.getRestfulServer().registerInterceptor(new AddResourceCountsInterceptor("OperationDefinition"));
+			myServer.getRestfulServer().registerInterceptor(new OpenApiInterceptor());
+
+			String url = "http://localhost:" + myServer.getPort() + "/fhir/swagger-ui/";
+			String resp = fetchSwaggerUi(url);
+			List<String> buttonTexts = parsePageButtonTexts(resp, url);
+			assertThat(buttonTexts.toString(), buttonTexts, Matchers.contains("All", "System Level Operations", "OperationDefinition 1", "Observation", "Patient"));
+		}
+
+	}
+
+	@Nested
+	class R5 extends BaseOpenApiInterceptorTest {
+
+		/**
+		 * A provider that uses a resource type not present in R4
+		 */
+		private MyTypeLevelActorDefinitionProviderR5 myActorDefinitionProvider = new MyTypeLevelActorDefinitionProviderR5();
 
 		@BeforeEach
-	public void before() {
-		myClient = HttpClientBuilder.create().build();
+		void beforeEach() {
+			myServer.registerProvider(myActorDefinitionProvider);
+			ServerCapabilityStatementProvider a = (ServerCapabilityStatementProvider) myServer.getRestfulServer().getServerConformanceProvider();
+			myServer.getRestfulServer().getServerConformanceProvider();
 		}
 
 		@AfterEach
-	public void after() throws IOException {
-		myClient.close();
+		void afterEach() {
+			myServer.unregisterProvider(myActorDefinitionProvider);
+		}
+
+		@Override
+		FhirContext getContext() {
+			return FhirContext.forR5Cached();
+		}
+	}
+
+
+	@SuppressWarnings("JUnitMalformedDeclaration")
+	abstract static class BaseOpenApiInterceptorTest {
+
+		@RegisterExtension
+		@Order(0)
+		protected RestfulServerExtension myServer = new RestfulServerExtension(getContext())
+			.withServletPath("/fhir/*")
+			.withServer(t -> t.registerProvider(new HashMapResourceProvider<>(getContext(), getContext().getResourceDefinition("Patient").getImplementingClass())))
+			.withServer(t -> t.registerProvider(new HashMapResourceProvider<>(getContext(), getContext().getResourceDefinition("Observation").getImplementingClass())))
+			.withServer(t -> t.registerProvider(new MySystemLevelOperationProvider()))
+			.withServer(t -> t.registerInterceptor(new ResponseHighlighterInterceptor()));
+		@RegisterExtension
+		private HttpClientExtension myClient = new HttpClientExtension();
+
+		abstract FhirContext getContext();
+
+		@AfterEach
+		public void after() {
 			myServer.getRestfulServer().getInterceptorService().unregisterAllInterceptors();
 		}
 
@@ -169,18 +207,6 @@ public class OpenApiInterceptorTest {
 
 		}
 
-
-	@Test
-	public void testSwaggerUiWithResourceCounts() throws IOException {
-		myServer.getRestfulServer().registerInterceptor(new AddResourceCountsInterceptor());
-		myServer.getRestfulServer().registerInterceptor(new OpenApiInterceptor());
-
-		String url = "http://localhost:" + myServer.getPort() + "/fhir/swagger-ui/";
-		String resp = fetchSwaggerUi(url);
-		List<String> buttonTexts = parsePageButtonTexts(resp, url);
-		assertThat(buttonTexts.toString(), buttonTexts, Matchers.contains("All", "System Level Operations", "Patient 2", "OperationDefinition 1", "Observation 0"));
-	}
-
 		@Test
 		public void testSwaggerUiWithCopyright() throws IOException {
 			myServer.getRestfulServer().registerInterceptor(new AddResourceCountsInterceptor());
@@ -249,17 +275,6 @@ public class OpenApiInterceptorTest {
 			assertThat(buttonTexts.toString(), buttonTexts, empty());
 		}
 
-	@Test
-	public void testSwaggerUiWithResourceCounts_OneResourceOnly() throws IOException {
-		myServer.getRestfulServer().registerInterceptor(new AddResourceCountsInterceptor("OperationDefinition"));
-		myServer.getRestfulServer().registerInterceptor(new OpenApiInterceptor());
-
-		String url = "http://localhost:" + myServer.getPort() + "/fhir/swagger-ui/";
-		String resp = fetchSwaggerUi(url);
-		List<String> buttonTexts = parsePageButtonTexts(resp, url);
-		assertThat(buttonTexts.toString(), buttonTexts, Matchers.contains("All", "System Level Operations", "OperationDefinition 1", "Observation", "Patient"));
-	}
-
 		@Test
 		public void testRemoveTrailingSlash() {
 			OpenApiInterceptor interceptor = new OpenApiInterceptor();
@@ -290,7 +305,7 @@ public class OpenApiInterceptorTest {
 			}
 		}
 
-	private String fetchSwaggerUi(String url) throws IOException {
+		protected String fetchSwaggerUi(String url) throws IOException {
 			String resp;
 			HttpGet get = new HttpGet(url);
 			try (CloseableHttpResponse response = myClient.execute(get)) {
@@ -301,7 +316,7 @@ public class OpenApiInterceptorTest {
 			return resp;
 		}
 
-	private List<String> parsePageButtonTexts(String resp, String url) throws IOException {
+		protected List<String> parsePageButtonTexts(String resp, String url) throws IOException {
 			HtmlPage html = HtmlUtil.parseAsHtml(resp, new URL(url));
 			HtmlDivision pageButtons = (HtmlDivision) html.getElementById("pageButtons");
 			if (pageButtons == null) {
@@ -326,28 +341,41 @@ public class OpenApiInterceptorTest {
 
 			@Hook(Pointcut.SERVER_CAPABILITY_STATEMENT_GENERATED)
 			public void capabilityStatementGenerated(IBaseConformance theCapabilityStatement) {
-			CapabilityStatement cs = (CapabilityStatement) theCapabilityStatement;
+				if (theCapabilityStatement instanceof org.hl7.fhir.r4.model.CapabilityStatement) {
+					org.hl7.fhir.r4.model.CapabilityStatement cs = (org.hl7.fhir.r4.model.CapabilityStatement) theCapabilityStatement;
 					cs.setCopyright("This server is copyright **Example Org** 2021");
-
 					int numResources = cs.getRestFirstRep().getResource().size();
 					for (int i = 0; i < numResources; i++) {
-
-				CapabilityStatement.CapabilityStatementRestResourceComponent restResource = cs.getRestFirstRep().getResource().get(i);
+						org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent restResource = cs.getRestFirstRep().getResource().get(i);
 						if (!myResourceNamesToAddTo.isEmpty() && !myResourceNamesToAddTo.contains(restResource.getType())) {
 							continue;
 						}
-
 						restResource.addExtension(
 							ExtensionConstants.CONF_RESOURCE_COUNT,
-					new DecimalType(i) // reverse order
+							new org.hl7.fhir.r4.model.DecimalType(i) // reverse order
 						);
-
+					}
+				} else {
+					org.hl7.fhir.r5.model.CapabilityStatement cs = (org.hl7.fhir.r5.model.CapabilityStatement) theCapabilityStatement;
+					cs.setCopyright("This server is copyright **Example Org** 2021");
+					int numResources = cs.getRestFirstRep().getResource().size();
+					for (int i = 0; i < numResources; i++) {
+						org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent restResource = cs.getRestFirstRep().getResource().get(i);
+						if (!myResourceNamesToAddTo.isEmpty() && !myResourceNamesToAddTo.contains(restResource.getType())) {
+							continue;
+						}
+						restResource.addExtension(
+							ExtensionConstants.CONF_RESOURCE_COUNT,
+							new org.hl7.fhir.r5.model.DecimalType(i) // reverse order
+						);
+					}
 				}
 			}
 
 		}
+	}
 
-	public static class MyLastNProvider {
+	public static class MySystemLevelOperationProvider {
 
 
 		@Description(value = "LastN Description", shortDefinition = "LastN Short")
@@ -375,11 +403,35 @@ public class OpenApiInterceptorTest {
 			throw new IllegalStateException();
 		}
 
-		@Patch(type = Patient.class)
+		@Patch(typeName = "Patient")
 		public MethodOutcome patch(HttpServletRequest theRequest, @IdParam IIdType theId, @ConditionalUrlParam String theConditionalUrl, RequestDetails theRequestDetails, @ResourceParam String theBody, PatchTypeEnum thePatchType, @ResourceParam IBaseParameters theRequestBody) {
 			throw new IllegalStateException();
 		}
 
+	}
+
+
+	static class MyTypeLevelActorDefinitionProviderR5 extends HashMapResourceProvider<ActorDefinition> {
+
+		/**
+		 * Constructor
+		 */
+		public MyTypeLevelActorDefinitionProviderR5() {
+			super(FhirContext.forR5Cached(), ActorDefinition.class);
+		}
+
+
+		@Validate
+		public MethodOutcome validate(
+			@ResourceParam IBaseResource theResource,
+			@ResourceParam String theRawResource,
+			@ResourceParam EncodingEnum theEncoding,
+			@Validate.Mode ValidationModeEnum theMode,
+			@Validate.Profile String theProfile,
+			RequestDetails theRequestDetails) {
+			return null;
+		}
 
 	}
+
 }

hapi-fhir-server-openapi/src/test/java/ca/uhn/fhir/rest/openapi/OpenApiInterceptorWithAuthorizationInterceptorTest.java

@@ -42,7 +42,7 @@ public class OpenApiInterceptorWithAuthorizationInterceptorTest {
 		.withServletPath("/fhir/*")
 		.withServer(t -> t.registerProvider(new HashMapResourceProvider<>(myFhirContext, Patient.class)))
 		.withServer(t -> t.registerProvider(new HashMapResourceProvider<>(myFhirContext, Observation.class)))
-		.withServer(t -> t.registerProvider(new OpenApiInterceptorTest.MyLastNProvider()))
+		.withServer(t -> t.registerProvider(new OpenApiInterceptorTest.MySystemLevelOperationProvider()))
 		.withServer(t -> t.registerInterceptor(new ResponseHighlighterInterceptor()));
 	private CloseableHttpClient myClient;
 	private AuthorizationInterceptor myAuthorizationInterceptor;

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseOutcomeReturningMethodBindingWithResourceIdButNoResourceBody.java

@@ -28,6 +28,8 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import java.lang.reflect.Method;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 public abstract class BaseOutcomeReturningMethodBindingWithResourceIdButNoResourceBody
 		extends BaseOutcomeReturningMethodBinding {
 
@@ -39,13 +41,16 @@ public abstract class BaseOutcomeReturningMethodBindingWithResourceIdButNoResour
 			FhirContext theContext,
 			Object theProvider,
 			Class<?> theMethodAnnotationType,
-			Class<? extends IBaseResource> theResourceTypeFromAnnotation) {
+			Class<? extends IBaseResource> theResourceTypeFromAnnotation,
+			String theResourceTypeNameFromAnnotation) {
 		super(theMethod, theContext, theMethodAnnotationType, theProvider);
 
 		Class<? extends IBaseResource> resourceType = theResourceTypeFromAnnotation;
 		if (resourceType != IBaseResource.class) {
 			RuntimeResourceDefinition def = theContext.getResourceDefinition(resourceType);
 			myResourceName = def.getName();
+		} else if (isNotBlank(theResourceTypeNameFromAnnotation)) {
+			myResourceName = theResourceTypeNameFromAnnotation;
 		} else {
 			if (theProvider != null && theProvider instanceof IResourceProvider) {
 				RuntimeResourceDefinition def =
@@ -56,7 +61,7 @@ public abstract class BaseOutcomeReturningMethodBindingWithResourceIdButNoResour
 						Msg.code(457) + "Can not determine resource type for method '" + theMethod.getName()
 								+ "' on type " + theMethod.getDeclaringClass().getCanonicalName()
 								+ " - Did you forget to include the resourceType() value on the @"
-								+ Delete.class.getSimpleName() + " method annotation?");
+								+ theMethodAnnotationType.getSimpleName() + " method annotation?");
 			}
 		}
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/DeleteMethodBinding.java

@@ -38,7 +38,8 @@ public class DeleteMethodBinding extends BaseOutcomeReturningMethodBindingWithRe
 				theContext,
 				theProvider,
 				Delete.class,
-				theMethod.getAnnotation(Delete.class).type());
+				theMethod.getAnnotation(Delete.class).type(),
+				theMethod.getAnnotation(Delete.class).typeName());
 	}
 
 	@Nonnull

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/PatchMethodBinding.java

@@ -54,7 +54,8 @@ public class PatchMethodBinding extends BaseOutcomeReturningMethodBindingWithRes
 				theContext,
 				theProvider,
 				Patch.class,
-				theMethod.getAnnotation(Patch.class).type());
+				theMethod.getAnnotation(Patch.class).type(),
+				theMethod.getAnnotation(Patch.class).typeName());
 
 		for (ListIterator<Class<?>> iter =
 						Arrays.asList(theMethod.getParameterTypes()).listIterator();

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/server/RestfulServerExtension.java

@@ -29,12 +29,11 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.server.IPagingProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
-import ca.uhn.fhir.validation.FhirValidator;
-import ca.uhn.fhir.validation.ResultSeverityEnum;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.time.DateUtils;
 import org.junit.jupiter.api.extension.ExtensionContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.servlet.http.HttpServlet;
 import java.util.ArrayList;
@@ -45,6 +44,7 @@ import java.util.Map;
 import java.util.function.Consumer;
 
 public class RestfulServerExtension extends BaseJettyServerExtension<RestfulServerExtension> {
+	private static final Logger ourLog = LoggerFactory.getLogger(RestfulServerExtension.class);
 	private FhirContext myFhirContext;
 	private List<Object> myProviders = new ArrayList<>();
 	private FhirVersionEnum myFhirVersion;
@@ -86,6 +86,8 @@ public class RestfulServerExtension extends BaseJettyServerExtension<RestfulServ
 
 		myFhirContext.getRestfulClientFactory().setSocketTimeout((int) (500 * DateUtils.MILLIS_PER_SECOND));
 		myFhirContext.getRestfulClientFactory().setServerValidationMode(myServerValidationMode);
+
+		ourLog.info("FHIR server has been started with base URL: {}", getBaseUrl());
 	}
 
 	@Override