Support GraphQL for R3/4/5 (#1424)

* Work on grpahql enhanbcements

* Add some more chars to the sanitizer function

* Add changelog

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java

@@ -163,7 +163,16 @@ public class UrlUtil {
 		if (theString != null) {
 			for (int i = 0; i < theString.length(); i++) {
 				char nextChar = theString.charAt(i);
-				if (nextChar == '<' || nextChar == '"') {
+				switch (nextChar) {
+					case '\'':
+					case '"':
+					case '<':
+					case '>':
+					case '\n':
+					case '\r':
+						return true;
+				}
+				if (nextChar < ' ') {
 					return true;
 				}
 			}
@@ -348,7 +357,17 @@ public class UrlUtil {
 
 	/**
 	 * This method specifically HTML-encodes the &quot; and
-	 * &lt; characters in order to prevent injection attacks
+	 * &lt; characters in order to prevent injection attacks.
+	 *
+	 * The following characters are escaped:
+	 * <ul>
+	 *    <li>&apos;</li>
+	 *    <li>&quot;</li>
+	 *    <li>&lt;</li>
+	 *    <li>&gt;</li>
+	 *    <li>\n (newline)</li>
+	 * </ul>
+	 *
 	 */
 	public static String sanitizeUrlPart(CharSequence theString) {
 		if (theString == null) {
@@ -364,6 +383,10 @@ public class UrlUtil {
 
 				char nextChar = theString.charAt(j);
 				switch (nextChar) {
+					/*
+					 * NB: If you add a constant here, you also need to add it
+					 * to isNeedsSanitization()!!
+					 */
 					case '\'':
 						buffer.append("&apos;");
 						break;
@@ -373,8 +396,19 @@ public class UrlUtil {
 					case '<':
 						buffer.append("&lt;");
 						break;
+					case '>':
+						buffer.append("&gt;");
+						break;
+					case '\n':
+						buffer.append("&#10;");
+						break;
+					case '\r':
+						buffer.append("&#13;");
+						break;
 					default:
-						buffer.append(nextChar);
+						if (nextChar >= ' ') {
+							buffer.append(nextChar);
+						}
 						break;
 				}
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/UrlUtilTest.java

@@ -59,4 +59,15 @@ public class UrlUtilTest {
 
 	}
 
+	@Test
+	public void testSanitize() {
+		assertEquals(" ' ", UrlUtil.sanitizeUrlPart(" ' "));
+		assertEquals(" &lt; ", UrlUtil.sanitizeUrlPart(" < "));
+		assertEquals(" &gt; ", UrlUtil.sanitizeUrlPart(" > "));
+		assertEquals(" &quot; ", UrlUtil.sanitizeUrlPart(" \" "));
+		assertEquals(" &#10; ", UrlUtil.sanitizeUrlPart(" \n "));
+		assertEquals(" &#13; ", UrlUtil.sanitizeUrlPart(" \r "));
+		assertEquals("  ", UrlUtil.sanitizeUrlPart(" \0 "));
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -24,10 +24,8 @@ import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
-import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
-import org.hl7.fhir.r4.hapi.rest.server.GraphQLProvider;
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.interceptor.executor.InterceptorService;
 import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
 import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
@@ -23,6 +24,7 @@ import ca.uhn.fhir.jpa.subscription.module.matcher.ISubscriptionMatcher;
 import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
 import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
 import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.*;
@@ -109,6 +111,12 @@ public abstract class BaseConfig implements SchedulingConfigurer {
 
 	public abstract FhirContext fhirContext();
 
+	@Bean
+	@Lazy
+	public IGraphQLStorageServices graphqlStorageServices() {
+		return new JpaStorageServices();
+	}
+
 	@Bean
 	public ScheduledExecutorFactoryBean scheduledExecutorService() {
 		ScheduledExecutorFactoryBean b = new ScheduledExecutorFactoryBean();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
@@ -73,6 +74,12 @@ public class BaseDstu3Config extends BaseConfig {
 		return retVal;
 	}
 
+	@Bean(name = GRAPHQL_PROVIDER_NAME)
+	@Lazy
+	public GraphQLProvider graphQLProvider() {
+		return new GraphQLProvider(fhirContextDstu3(), validationSupportChainDstu3(), graphqlStorageServices());
+	}
+
 	@Bean
 	public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
 		return new TransactionProcessorVersionAdapterDstu3();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java

@@ -21,12 +21,13 @@ import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r4.hapi.rest.server.GraphQLProvider;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import org.hl7.fhir.r4.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.utils.GraphQLEngine;
 import org.hl7.fhir.r5.utils.IResourceValidator;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -91,12 +92,6 @@ public class BaseR4Config extends BaseConfig {
 		return new GraphQLProvider(fhirContextR4(), validationSupportChainR4(), graphqlStorageServices());
 	}
 
-	@Bean
-	@Lazy
-	public GraphQLEngine.IGraphQLStorageServices graphqlStorageServices() {
-		return new JpaStorageServices();
-	}
-
 	@Bean(name = "myInstanceValidatorR4")
 	@Lazy
 	public IValidatorModule instanceValidatorR4() {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java

@@ -8,7 +8,7 @@ import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.r5.TransactionProcessorVersionAdapterR5;
-import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR5;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR5;
@@ -21,11 +21,9 @@ import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR5;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r5.hapi.rest.server.GraphQLProvider;
 import org.hl7.fhir.r5.hapi.validation.CachingValidationSupport;
 import org.hl7.fhir.r5.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.r5.model.Bundle;
-import org.hl7.fhir.r5.utils.GraphQLEngine;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
@@ -85,17 +83,11 @@ public class BaseR5Config extends BaseConfig {
 		return new TransactionProcessor<>();
 	}
 
-//	@Bean(name = GRAPHQL_PROVIDER_NAME)
+	@Bean(name = GRAPHQL_PROVIDER_NAME)
-//	@Lazy
+	@Lazy
-//	public GraphQLProvider graphQLProvider() {
+	public GraphQLProvider graphQLProvider() {
-//		return new GraphQLProvider(fhirContextR5(), validationSupportChainR5(), graphqlStorageServices());
+		return new GraphQLProvider(fhirContextR5(), validationSupportChainR5(), graphqlStorageServices());
-//	}
+	}
-//
-//	@Bean
-//	@Lazy
-//	public GraphQLEngine.IGraphQLStorageServices graphqlStorageServices() {
-//		return new JpaStorageServices();
-//	}
 
 	@Bean(name = "myInstanceValidatorR5")
 	@Lazy

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/JpaStorageServices.java

@@ -24,7 +24,6 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -33,22 +32,21 @@ import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseReference;
 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.IdType;
-import org.hl7.fhir.r4.model.Reference;
-import org.hl7.fhir.r4.model.Resource;
-import org.hl7.fhir.r4.utils.GraphQLEngine;
 import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.graphql.Value;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 import java.util.List;
 
-public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implements GraphQLEngine.IGraphQLStorageServices {
+public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implements IGraphQLStorageServices {
 
+	private static final int MAX_SEARCH_SIZE = 500;
 
 	private IFhirResourceDao<? extends IBaseResource> getDao(String theResourceType) {
 		RuntimeResourceDefinition typeDef = getContext().getResourceDefinition(theResourceType);
@@ -57,13 +55,13 @@ public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implement
 
 	@Transactional(propagation = Propagation.NEVER)
 	@Override
-	public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<Resource> theMatches) throws FHIRException {
+	public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
 
 		RuntimeResourceDefinition typeDef = getContext().getResourceDefinition(theType);
 		IFhirResourceDao<? extends IBaseResource> dao = getDao(typeDef.getImplementingClass());
 
 		SearchParameterMap params = new SearchParameterMap();
-		params.setLoadSynchronousUpTo(500);
+		params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
 
 		for (Argument nextArgument : theSearchParams) {
 
@@ -114,40 +112,37 @@ public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implement
 			size = response.preferredPageSize();
 		}
 
-		for (IBaseResource next : response.getResources(0, size)) {
+		theMatches.addAll(response.getResources(0, size));
-			theMatches.add((Resource) next);
-		}
 
 	}
 
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
-	public Resource lookup(Object theAppInfo, String theType, String theId) throws FHIRException {
+	public IBaseResource lookup(Object theAppInfo, String theType, String theId) throws FHIRException {
 		IIdType refId = getContext().getVersion().newIdType();
 		refId.setValue(theType + "/" + theId);
 		return lookup(theAppInfo, refId);
 	}
 
-	private Resource lookup(Object theAppInfo, IIdType theRefId) {
+	private IBaseResource lookup(Object theAppInfo, IIdType theRefId) {
 		IFhirResourceDao<? extends IBaseResource> dao = getDao(theRefId.getResourceType());
 		RequestDetails requestDetails = (RequestDetails) theAppInfo;
-		return (Resource) dao.read(theRefId, requestDetails, false);
+		return dao.read(theRefId, requestDetails, false);
 	}
 
 	@Transactional(propagation = Propagation.REQUIRED)
-    @Override
+	@Override
-	public ReferenceResolution lookup(Object theAppInfo, Resource theContext, Reference theReference) throws FHIRException {
+	public ReferenceResolution lookup(Object theAppInfo, IBaseResource theContext, IBaseReference theReference) throws FHIRException {
-		IdType refId = new IdType(theReference.getReference());
+		IBaseResource outcome = lookup(theAppInfo, theReference.getReferenceElement());
-		Resource outcome = lookup(theAppInfo, refId);
 		if (outcome == null) {
-		return null;
+			return null;
-	}
+		}
 		return new ReferenceResolution(theContext, outcome);
 	}
 
 	@Transactional(propagation = Propagation.NEVER)
 	@Override
-	public Bundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
+	public IBaseBundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
 		throw new NotImplementedOperationException("Not yet able to handle this GraphQL request");
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/GraphQLProvider.java

@@ -0,0 +1,165 @@
+package ca.uhn.fhir.jpa.provider;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * 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%
+ */
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.support.IContextValidationSupport;
+import ca.uhn.fhir.rest.annotation.GraphQL;
+import ca.uhn.fhir.rest.annotation.GraphQLQuery;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Initialize;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.UnclassifiedServerFailureException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import org.apache.commons.lang3.ObjectUtils;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
+import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.utilities.graphql.IGraphQLEngine;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
+import org.hl7.fhir.utilities.graphql.ObjectValue;
+import org.hl7.fhir.utilities.graphql.Parser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.util.function.Supplier;
+
+public class GraphQLProvider {
+	private final Supplier<IGraphQLEngine> engineFactory;
+	private final IGraphQLStorageServices myStorageServices;
+	private Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
+
+	/**
+	 * Constructor which uses a default context and validation support object
+	 *
+	 * @param theStorageServices The storage services (this object will be used to retrieve various resources as required by the GraphQL engine)
+	 */
+	public GraphQLProvider(IGraphQLStorageServices theStorageServices) {
+		this(FhirContext.forR4(), null, theStorageServices);
+	}
+
+	/**
+	 * Constructor which uses the given worker context
+	 *
+	 * @param theFhirContext       The HAPI FHIR Context object
+	 * @param theValidationSupport The HAPI Validation Support object, or null
+	 * @param theStorageServices   The storage services (this object will be used to retrieve various resources as required by the GraphQL engine)
+	 */
+	public GraphQLProvider(@Nonnull FhirContext theFhirContext, @Nullable IContextValidationSupport theValidationSupport, @Nonnull IGraphQLStorageServices theStorageServices) {
+		Validate.notNull(theFhirContext, "theFhirContext must not be null");
+		Validate.notNull(theStorageServices, "theStorageServices must not be null");
+
+		switch (theFhirContext.getVersion().getVersion()) {
+			case DSTU3: {
+				IValidationSupport validationSupport = (IValidationSupport) theValidationSupport;
+				validationSupport = ObjectUtils.defaultIfNull(validationSupport, new org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport());
+				org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext workerContext = new org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext(theFhirContext, validationSupport);
+				engineFactory = () -> new org.hl7.fhir.dstu3.utils.GraphQLEngine(workerContext);
+				break;
+			}
+			case R4: {
+				org.hl7.fhir.r4.hapi.ctx.IValidationSupport validationSupport = (org.hl7.fhir.r4.hapi.ctx.IValidationSupport) theValidationSupport;
+				validationSupport = ObjectUtils.defaultIfNull(validationSupport, new org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport());
+				org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext workerContext = new org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext(theFhirContext, validationSupport);
+				engineFactory = () -> new org.hl7.fhir.r4.utils.GraphQLEngine(workerContext);
+				break;
+			}
+			case R5: {
+				org.hl7.fhir.r5.hapi.ctx.IValidationSupport validationSupport = (org.hl7.fhir.r5.hapi.ctx.IValidationSupport) theValidationSupport;
+				validationSupport = ObjectUtils.defaultIfNull(validationSupport, new org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport());
+				org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext workerContext = new org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext(theFhirContext, validationSupport);
+				engineFactory = () -> new org.hl7.fhir.r5.utils.GraphQLEngine(workerContext);
+				break;
+			}
+			case DSTU2:
+			case DSTU2_HL7ORG:
+			case DSTU2_1:
+			default: {
+				throw new UnsupportedOperationException("GraphQL not supported for version: " + theFhirContext.getVersion().getVersion());
+			}
+		}
+
+		myStorageServices = theStorageServices;
+	}
+
+	@GraphQL
+	public String processGraphQlRequet(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQuery String theQuery) {
+
+		IGraphQLEngine engine = engineFactory.get();
+		engine.setAppInfo(theRequestDetails);
+		engine.setServices(myStorageServices);
+		try {
+			engine.setGraphQL(Parser.parse(theQuery));
+		} catch (Exception theE) {
+			throw new InvalidRequestException("Unable to parse GraphQL Expression: " + theE.toString());
+		}
+
+		try {
+
+			if (theId != null) {
+				IBaseResource focus = myStorageServices.lookup(theRequestDetails, theId.getResourceType(), theId.getIdPart());
+				engine.setFocus(focus);
+			}
+			engine.execute();
+
+			StringBuilder outputBuilder = new StringBuilder();
+			ObjectValue output = engine.getOutput();
+			output.write(outputBuilder, 0, "\n");
+
+			return outputBuilder.toString();
+
+		} catch (Exception e) {
+			StringBuilder b = new StringBuilder();
+			b.append("Unable to execute GraphQL Expression: ");
+			int statusCode = 500;
+			if (e instanceof BaseServerResponseException) {
+				b.append("HTTP ");
+				statusCode = ((BaseServerResponseException) e).getStatusCode();
+				b.append(statusCode);
+				b.append(" ");
+			} else {
+				// This means it's a bug, so let's log
+				ourLog.error("Failure during GraphQL processing", e);
+			}
+			b.append(e.getMessage());
+			throw new UnclassifiedServerFailureException(statusCode, b.toString());
+		}
+	}
+
+	@Initialize
+	public void initialize(RestfulServer theServer) {
+		ourLog.trace("Initializing GraphQL provider");
+		if (!theServer.getFhirContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
+			throw new ConfigurationException("Can not use " + getClass().getName() + " provider on server with FHIR " + theServer.getFhirContext().getVersion().getVersion().name() + " context");
+		}
+	}
+
+
+}
+

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/GraphQLR4ProviderTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.rest.server;
+package ca.uhn.fhir.jpa.provider;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
@@ -6,6 +6,10 @@ import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.test.utilities.JettyUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.io.IOUtils;
@@ -18,11 +22,14 @@ import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.hapi.rest.server.GraphQLProvider;
+import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.HumanName;
-import org.hl7.fhir.r4.utils.GraphQLEngine;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -34,9 +41,8 @@ import java.util.List;
 import java.util.concurrent.TimeUnit;
 
 import static org.hamcrest.Matchers.startsWith;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-
+import static org.junit.Assert.assertThat;
-import ca.uhn.fhir.test.utilities.JettyUtil;
 
 public class GraphQLR4ProviderTest {
 
@@ -216,9 +222,9 @@ public class GraphQLR4ProviderTest {
 
 	}
 
-	private static class MyStorageServices implements GraphQLEngine.IGraphQLStorageServices {
+	private static class MyStorageServices implements IGraphQLStorageServices {
 		@Override
-		public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<Resource> theMatches) throws FHIRException {
+		public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
 			ourLog.info("listResources of {} - {}", theType, theSearchParams);
 
 			if (theSearchParams.size() == 1) {
@@ -264,8 +270,8 @@ public class GraphQLR4ProviderTest {
 		}
 
 		@Override
-		public ReferenceResolution lookup(Object theAppInfo, Resource theContext, Reference theReference) throws FHIRException {
+		public IGraphQLStorageServices.ReferenceResolution lookup(Object theAppInfo, IBaseResource theContext, IBaseReference theReference) throws FHIRException {
-			ourLog.info("lookup from {} to {}", theContext.getIdElement().getValue(), theReference.getReference());
+			ourLog.info("lookup from {} to {}", theContext.getIdElement().getValue(), theReference.getReferenceElement().getValue());
 			return null;
 		}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider.dstu3;
 import ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
@@ -97,6 +98,8 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			SubscriptionTriggeringProvider subscriptionTriggeringProvider = myAppCtx.getBean(SubscriptionTriggeringProvider.class);
 			ourRestServer.registerProvider(subscriptionTriggeringProvider);
 
+			ourRestServer.registerProvider(myAppCtx.getBean(GraphQLProvider.class));
+
 			JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(ourRestServer, mySystemDao, myDaoConfig);
 			confProvider.setImplementationDescription("THIS IS THE DESC");
 			ourRestServer.setServerConformanceProvider(confProvider);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/GraphQLProviderDstu3Test.java

@@ -0,0 +1,92 @@
+package ca.uhn.fhir.jpa.provider.dstu3;
+
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.util.UrlUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+
+import static org.junit.Assert.assertEquals;
+
+public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
+	private Logger ourLog = LoggerFactory.getLogger(GraphQLProviderDstu3Test.class);
+	private IIdType myPatientId0;
+
+	@Test
+	public void testInstanceSimpleRead() throws IOException {
+		initTestPatients();
+
+		String query = "{name{family,given}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"name\":[{\n" +
+				"    \"family\":\"FAM\",\n" +
+				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"  },{\n" +
+				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"  }]\n" +
+				"}"), TestUtil.stripReturns(resp));
+		}
+
+	}
+
+	@Test
+	public void testSystemSimpleSearch() throws IOException {
+		initTestPatients();
+
+		String query = "{PatientList(given:\"given\"){name{family,given}}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"PatientList\":[{\n" +
+				"    \"name\":[{\n" +
+				"      \"family\":\"FAM\",\n" +
+				"      \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"    },{\n" +
+				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"    }]\n" +
+				"  },{\n" +
+				"    \"name\":[{\n" +
+				"      \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
+				"    }]\n" +
+				"  }]\n" +
+				"}"), TestUtil.stripReturns(resp));
+		}
+
+	}
+
+	private void initTestPatients() {
+		Patient p = new Patient();
+		p.addName()
+			.setFamily("FAM")
+			.addGiven("GIVEN1")
+			.addGiven("GIVEN2");
+		p.addName()
+			.addGiven("GivenOnly1")
+			.addGiven("GivenOnly2");
+		myPatientId0 = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addName()
+			.addGiven("GivenOnlyB1")
+			.addGiven("GivenOnlyB2");
+		ourClient.create().resource(p).execute();
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
@@ -71,7 +72,6 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 	protected IGenericClient ourClient;
 	ResourceCountCache ourResourceCountsCache;
 	private TerminologyUploaderProvider myTerminologyUploaderProvider;
-	private Object ourGraphQLProvider;
 	private boolean ourRestHookSubscriptionInterceptorRequested;
 
 	@Autowired
@@ -105,10 +105,10 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 			ourRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
 
 			myTerminologyUploaderProvider = myAppCtx.getBean(TerminologyUploaderProvider.class);
-			ourGraphQLProvider = myAppCtx.getBean("myGraphQLProvider");
 			myDaoRegistry = myAppCtx.getBean(DaoRegistry.class);
 
-			ourRestServer.registerProviders(mySystemProvider, myTerminologyUploaderProvider, ourGraphQLProvider);
+			ourRestServer.registerProviders(mySystemProvider, myTerminologyUploaderProvider);
+			ourRestServer.registerProvider(myAppCtx.getBean(GraphQLProvider.class));
 
 			JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(ourRestServer, mySystemDao, myDaoConfig);
 			confProvider.setImplementationDescription("THIS IS THE DESC");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLProviderR4Test.java

@@ -27,20 +27,17 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 		String query = "{name{family,given}}";
 		HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
 
-		CloseableHttpResponse response = ourHttpClient.execute(httpGet);
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
-		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
-			assertEquals(TestUtil.stripReturns(resp), TestUtil.stripReturns("{\n" +
+			assertEquals(TestUtil.stripReturns("{\n" +
 				"  \"name\":[{\n" +
 				"    \"family\":\"FAM\",\n" +
 				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
 				"  },{\n" +
 				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
 				"  }]\n" +
-				"}"));
+				"}"), TestUtil.stripReturns(resp));
-		} finally {
-			IOUtils.closeQuietly(response);
 		}
 
 	}
@@ -52,8 +49,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 		String query = "{PatientList(given:\"given\"){name{family,given}}}";
 		HttpGet httpGet = new HttpGet(ourServerBase + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
 
-		CloseableHttpResponse response = ourHttpClient.execute(httpGet);
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
-		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			assertEquals(TestUtil.stripReturns("{\n" +
@@ -70,10 +66,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
 				"    }]\n" +
 				"  }]\n" +
 				"}"), TestUtil.stripReturns(resp));
-		} finally {
-			IOUtils.closeQuietly(response);
 		}
-
 	}
 
 	private void initTestPatients() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/BaseResourceProviderR5Test.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig;
 import ca.uhn.fhir.jpa.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.r5.BaseJpaR5Test;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
@@ -108,8 +109,7 @@ public abstract class BaseResourceProviderR5Test extends BaseJpaR5Test {
 			myDaoRegistry = myAppCtx.getBean(DaoRegistry.class);
 			ourRestServer.registerProviders(mySystemProvider, myTerminologyUploaderProvider);
 
-//			ourGraphQLProvider = myAppCtx.getBean("myGraphQLProvider");
+			ourRestServer.registerProvider(myAppCtx.getBean(GraphQLProvider.class));
-//			ourRestServer.registerProvider(ourGraphQLProvider);
 
 			JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(ourRestServer, mySystemDao, myDaoConfig);
 			confProvider.setImplementationDescription("THIS IS THE DESC");

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -34,7 +34,7 @@ import ca.uhn.fhirtest.config.TestR4Config;
 import ca.uhn.fhirtest.config.TestR5Config;
 import ca.uhn.hapi.converters.server.VersionedApiConverterInterceptor;
 import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.r4.hapi.rest.server.GraphQLProvider;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
 import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
@@ -127,6 +127,7 @@ public class TestRestfulServer extends RestfulServer {
 				confProvider.setImplementationDescription(implDesc);
 				setServerConformanceProvider(confProvider);
 				providers.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
+				providers.add(myAppCtx.getBean(GraphQLProvider.class));
 				break;
 			}
 			case "R4": {
@@ -164,7 +165,7 @@ public class TestRestfulServer extends RestfulServer {
 				confProvider.setImplementationDescription(implDesc);
 				setServerConformanceProvider(confProvider);
 				providers.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
-//				providers.add(myAppCtx.getBean(GraphQLProvider.class));
+				providers.add(myAppCtx.getBean(GraphQLProvider.class));
 				break;
 			}
 			default:

hapi-fhir-server/pom.xml

@@ -19,6 +19,11 @@
 			<artifactId>hapi-fhir-base</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>org.hl7.fhir.utilities</artifactId>
+			<version>${fhir_core_version}</version>
+		</dependency>
 
 		<!-- Server -->
 		<dependency>

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/GraphQLProvider.java

@@ -1,107 +0,0 @@
-package org.hl7.fhir.r4.hapi.rest.server;
-
-import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.rest.annotation.GraphQL;
-import ca.uhn.fhir.rest.annotation.GraphQLQuery;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.Initialize;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.UnclassifiedServerFailureException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.context.IWorkerContext;
-import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
-import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
-import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r4.model.Resource;
-import org.hl7.fhir.r4.utils.GraphQLEngine;
-import org.hl7.fhir.utilities.graphql.ObjectValue;
-import org.hl7.fhir.utilities.graphql.Parser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class GraphQLProvider {
-  private final IWorkerContext myWorkerContext;
-  private Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
-  private GraphQLEngine.IGraphQLStorageServices myStorageServices;
-
-  /**
-   * Constructor which uses a default context and validation support object
-   *
-   * @param theStorageServices The storage services (this object will be used to retrieve various resources as required by the GraphQL engine)
-   */
-  public GraphQLProvider(GraphQLEngine.IGraphQLStorageServices theStorageServices) {
-    this(FhirContext.forR4(), new DefaultProfileValidationSupport(), theStorageServices);
-  }
-
-  /**
-   * Constructor which uses the given worker context
-   *
-   * @param theFhirContext       The HAPI FHIR Context object
-   * @param theValidationSupport The HAPI Validation Support object
-   * @param theStorageServices   The storage services (this object will be used to retrieve various resources as required by the GraphQL engine)
-   */
-  public GraphQLProvider(FhirContext theFhirContext, IValidationSupport theValidationSupport, GraphQLEngine.IGraphQLStorageServices theStorageServices) {
-    myWorkerContext = new HapiWorkerContext(theFhirContext, theValidationSupport);
-    myStorageServices = theStorageServices;
-  }
-
-  @GraphQL
-  public String graphql(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQuery String theQuery) {
-
-    GraphQLEngine engine = new GraphQLEngine(myWorkerContext);
-    engine.setAppInfo(theRequestDetails);
-    engine.setServices(myStorageServices);
-    try {
-      engine.setGraphQL(Parser.parse(theQuery));
-    } catch (Exception theE) {
-      throw new InvalidRequestException("Unable to parse GraphQL Expression: " + theE.toString());
-    }
-
-    try {
-
-      if (theId != null) {
-        Resource focus = myStorageServices.lookup(theRequestDetails, theId.getResourceType(), theId.getIdPart());
-        engine.setFocus(focus);
-      }
-      engine.execute();
-
-      StringBuilder outputBuilder = new StringBuilder();
-      ObjectValue output = engine.getOutput();
-      output.write(outputBuilder, 0, "\n");
-
-      return outputBuilder.toString();
-
-    } catch (Exception e) {
-      StringBuilder b = new StringBuilder();
-      b.append("Unable to execute GraphQL Expression: ");
-      int statusCode = 500;
-      if (e instanceof BaseServerResponseException) {
-        b.append("HTTP ");
-        statusCode = ((BaseServerResponseException) e).getStatusCode();
-        b.append(statusCode);
-        b.append(" ");
-      } else {
-        // This means it's a bug, so let's log
-        ourLog.error("Failure during GraphQL processing", e);
-      }
-      b.append(e.getMessage());
-      throw new UnclassifiedServerFailureException(statusCode, b.toString());
-    }
-  }
-
-  @Initialize
-  public void initialize(RestfulServer theServer) {
-    ourLog.trace("Initializing GraphQL provider");
-    if (theServer.getFhirContext().getVersion().getVersion() != FhirVersionEnum.R4) {
-      throw new ConfigurationException("Can not use " + getClass().getName() + " provider on server with FHIR " + theServer.getFhirContext().getVersion().getVersion().name() + " context");
-    }
-  }
-
-
-}
-

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/GraphQLEngineTest.java

@@ -16,7 +16,6 @@ import java.io.IOException;
 
 import static org.junit.Assert.assertEquals;
 import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -33,8 +32,8 @@ public class GraphQLEngineTest {
 		return obs;
 	}
 
-	private GraphQLEngine.IGraphQLStorageServices createStorageServices() throws FHIRException {
+	private IGraphQLStorageServices createStorageServices() throws FHIRException {
-		GraphQLEngine.IGraphQLStorageServices retVal = mock(GraphQLEngine.IGraphQLStorageServices.class);
+		IGraphQLStorageServices retVal = mock(IGraphQLStorageServices.class);
 		when(retVal.lookup(nullable(Object.class), nullable(Resource.class), nullable(Reference.class))).thenAnswer(new Answer<Object>() {
 			@Override
 			public Object answer(InvocationOnMock invocation) {
@@ -46,7 +45,7 @@ public class GraphQLEngineTest {
 				if (reference.getReference().equalsIgnoreCase("Patient/123")) {
 					Patient p = new Patient();
 					p.getBirthDateElement().setValueAsString("2011-02-22");
-					return new GraphQLEngine.IGraphQLStorageServices.ReferenceResolution(context, p);
+					return new IGraphQLStorageServices.ReferenceResolution(context, p);
 				}
 
 				ourLog.info("Not found!");

hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/rest/server/GraphQLProvider.java

@@ -1,107 +0,0 @@
-package org.hl7.fhir.r5.hapi.rest.server;
-
-import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.rest.annotation.GraphQL;
-import ca.uhn.fhir.rest.annotation.GraphQLQuery;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.Initialize;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.UnclassifiedServerFailureException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r5.context.IWorkerContext;
-import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
-import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
-import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r5.model.Resource;
-import org.hl7.fhir.r5.utils.GraphQLEngine;
-import org.hl7.fhir.utilities.graphql.ObjectValue;
-import org.hl7.fhir.utilities.graphql.Parser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class GraphQLProvider {
-  private final IWorkerContext myWorkerContext;
-  private Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
-  private GraphQLEngine.IGraphQLStorageServices myStorageServices;
-
-  /**
-   * Constructor which uses a default context and validation support object
-   *
-   * @param theStorageServices The storage services (this object will be used to retrieve various resources as required by the GraphQL engine)
-   */
-  public GraphQLProvider(GraphQLEngine.IGraphQLStorageServices theStorageServices) {
-    this(FhirContext.forR5(), new DefaultProfileValidationSupport(), theStorageServices);
-  }
-
-  /**
-   * Constructor which uses the given worker context
-   *
-   * @param theFhirContext       The HAPI FHIR Context object
-   * @param theValidationSupport The HAPI Validation Support object
-   * @param theStorageServices   The storage services (this object will be used to retrieve various resources as required by the GraphQL engine)
-   */
-  public GraphQLProvider(FhirContext theFhirContext, IValidationSupport theValidationSupport, GraphQLEngine.IGraphQLStorageServices theStorageServices) {
-    myWorkerContext = new HapiWorkerContext(theFhirContext, theValidationSupport);
-    myStorageServices = theStorageServices;
-  }
-
-  @GraphQL
-  public String graphql(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQuery String theQuery) {
-
-    GraphQLEngine engine = new GraphQLEngine(myWorkerContext);
-    engine.setAppInfo(theRequestDetails);
-    engine.setServices(myStorageServices);
-    try {
-      engine.setGraphQL(Parser.parse(theQuery));
-    } catch (Exception theE) {
-      throw new InvalidRequestException("Unable to parse GraphQL Expression: " + theE.toString());
-    }
-
-    try {
-
-      if (theId != null) {
-        Resource focus = myStorageServices.lookup(theRequestDetails, theId.getResourceType(), theId.getIdPart());
-        engine.setFocus(focus);
-      }
-      engine.execute();
-
-      StringBuilder outputBuilder = new StringBuilder();
-      ObjectValue output = engine.getOutput();
-      output.write(outputBuilder, 0, "\n");
-
-      return outputBuilder.toString();
-
-    } catch (Exception e) {
-      StringBuilder b = new StringBuilder();
-      b.append("Unable to execute GraphQL Expression: ");
-      int statusCode = 500;
-      if (e instanceof BaseServerResponseException) {
-        b.append("HTTP ");
-        statusCode = ((BaseServerResponseException) e).getStatusCode();
-        b.append(statusCode);
-        b.append(" ");
-      } else {
-        // This means it's a bug, so let's log
-        ourLog.error("Failure during GraphQL processing", e);
-      }
-      b.append(e.getMessage());
-      throw new UnclassifiedServerFailureException(statusCode, b.toString());
-    }
-  }
-
-  @Initialize
-  public void initialize(RestfulServer theServer) {
-    ourLog.trace("Initializing GraphQL provider");
-    if (theServer.getFhirContext().getVersion().getVersion() != FhirVersionEnum.R5) {
-      throw new ConfigurationException("Can not use " + getClass().getName() + " provider on server with FHIR " + theServer.getFhirContext().getVersion().getVersion().name() + " context");
-    }
-  }
-
-
-}
-

src/changes/changes.xml

@@ -88,16 +88,28 @@
 			</action>
 			<action type="add">
 				Support for the new R5 draft resources has been added. This support includes the client,
+				<![CDATA[
+				<b>New Feature</b>:
 				server, and JPA server. Note that these definitions will change as the R5 standard is 
 				modified until it is released, so use with caution!
+				]]>
 			</action>
 			<action type="add">
+				<![CDATA[
+				<b>New Feature</b>:
 				A new interceptor called
-				<![CDATA[<code>ConsentInterceptor</code>]]> has been added. This interceptor allows
+				<code>ConsentInterceptor</code> has been added. This interceptor allows
 				JPA based servers to make appropriate consent decisions related to resources that
 				and operations that are being returned. See
-				<![CDATA[<a href="http://hapifhir.io/doc_rest_server_security.html">Server Security</a>]]>
+				<a href="http://hapifhir.io/doc_rest_server_security.html">Server Security</a>
 				for more information.
+				]]>
+			</action>
+			<action type="add">
+				<![CDATA[
+				<b>New Feature</b>:
+				The JPA server now supports GraphQL for DSTU3 / R4 / R5 servers.
+				]]>
 			</action>
 			<action type="add">
 				Several enhancements have been made to the <![CDATA[<code>AuthorizationInterceptor</code>]]>:
@@ -105,7 +117,8 @@
 				<ul>
 				<li>The interceptor now registers against the <code>STORAGE_PRESHOW_RESOURCES</code> interceptor hook,
 				which allows it to successfully authorize JPA operations that don't actually return resource content,
-				such as GraphQL responses.</li>
+				such as GraphQL responses, and resources that have been filtered using the <code>_elements</code>
+				parameter.</li>
 				<li>
 				</li>The rule list is now cached on a per-request basis, which should improve performance</ul>
 				]]>