GraphQL Introspection Support (#3348)

* Start working on graphql Schema

* Start testing

* Work on introspection

* Work on introspection

* Use integers for date ordinals

* Add changelog

* GraphQL updates

* Ongoing wrk

* Cleanup

* Bump core lib

* Add changelog

* Clean up dependencies

* CLeanup

* Add missing message

* Test fix

* Change to force CI

hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/Msg.java

@@ -25,7 +25,7 @@ public final class Msg {
 
 	/**
 	 * IMPORTANT: Please update the following comment after you add a new code
-	 * Last code value: 2034
+	 * Last code value: 2036
 	 */
 
 	private Msg() {}

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

@@ -0,0 +1,24 @@
+package ca.uhn.fhir.util;
+
+import java.util.function.Supplier;
+
+/**
+ * This is used to allow lazy parameter initialization for SLF4j - Hopefully
+ * a future version will allow lambda params
+ */
+public class MessageSupplier {
+    private Supplier<?> supplier;
+
+    public MessageSupplier(Supplier<?> supplier) {
+        this.supplier = supplier;
+    }
+
+    @Override
+    public String toString() {
+        return supplier.get().toString();
+    }
+
+    public static MessageSupplier msg(Supplier<?> supplier) {
+        return new MessageSupplier(supplier);
+    }
+}

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
+import javax.annotation.Nonnull;
 import java.io.CharArrayWriter;
 import java.nio.charset.StandardCharsets;
 import java.text.Normalizer;
@@ -105,4 +106,13 @@ public class StringUtil {
 		return theString.substring(0, theString.offsetByCodePoints(0, theCodePointCount));
 	}
 
+	@Nonnull
+	public static String prependLineNumbers(@Nonnull String theInput) {
+		StringBuilder schemaOutput = new StringBuilder();
+		int index = 0;
+		for (String next : theInput.split("\\n")) {
+			schemaOutput.append(index++).append(": ").append(next.replace("\r", "")).append("\n");
+		}
+		return schemaOutput.toString();
+	}
 }

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

@@ -0,0 +1,64 @@
+package ca.uhn.fhir.util;
+
+import ch.qos.logback.classic.spi.ILoggingEvent;
+import ch.qos.logback.core.Appender;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.mockito.ArgumentMatcher;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static ca.uhn.fhir.util.MessageSupplier.msg;
+import static org.mockito.ArgumentMatchers.argThat;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+public class MessageSupplierTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(MessageSupplierTest.class);
+	private Appender myMockAppender;
+	private ch.qos.logback.classic.Logger myLoggerRoot;
+
+	@AfterEach
+	public void after() {
+		myLoggerRoot.detachAppender(myMockAppender);
+	}
+
+	@SuppressWarnings("unchecked")
+	@BeforeEach
+	public void before() {
+
+		/*
+		 * This is a bit funky, but it's useful for verifying that the headers actually get logged
+		 */
+		myMockAppender = mock(Appender.class);
+		when(myMockAppender.getName()).thenReturn("MOCK");
+
+		Logger logger = LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);
+
+		myLoggerRoot = (ch.qos.logback.classic.Logger) logger;
+		myLoggerRoot.addAppender(myMockAppender);
+	}
+
+
+	@Test
+	public void testLog() {
+
+		ourLog.info("Hello: {}", msg(() -> "Goodbye"));
+
+		verify(myMockAppender, times(1)).doAppend(argThat((ArgumentMatcher<ILoggingEvent>) argument -> {
+			String formattedMessage = argument.getFormattedMessage();
+			System.out.flush();
+			System.out.println("** Got Message: " + formattedMessage);
+			System.out.flush();
+			return formattedMessage.equals("Hello: Goodbye");
+		}));
+
+
+	}
+
+
+}

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

@@ -64,4 +64,9 @@ public class StringUtilTest {
 		assertEquals("a/a", StringUtil.chompCharacter("a/a////", '/'));
 	}
 
+	@Test
+	public void testPrependLineNumbers() {
+		assertEquals("0: A\n1: B\n", StringUtil.prependLineNumbers("A\nB"));
+	}
+
 }

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3348-add-graphql-introspection.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 3348
+title: "The HAPI FHIR server GraphQL endpoints now support GraphQL introspection, making them
+  much easier to use with GraphQL-capable IDEs."

hapi-fhir-jpaserver-base/pom.xml

@@ -15,24 +15,6 @@
 	<name>HAPI FHIR JPA Server</name>
 
 	<dependencies>
-		<!--
-				<dependency>
-					<groupId>com.fasterxml.jackson.jaxrs</groupId>
-					<artifactId>jackson-jaxrs-json-provider</artifactId>
-					<version>${jackson.version}</version>
-				</dependency>
-				<dependency>
-					<groupId>com.fasterxml.jackson.datatype</groupId>
-					<artifactId>jackson-datatype-hibernate4</artifactId>
-					<version>${jackson.version}</version>
-				</dependency>
-
-				<dependency>
-					<groupId>org.apache.commons</groupId>
-					<artifactId>commons-lang3</artifactId>
-					<version>3.5</version>
-				</dependency>
-		-->
 
 		<dependency>
 			<groupId>com.fasterxml.woodstox</groupId>
@@ -174,6 +156,12 @@
 			<artifactId>javassist</artifactId>
 		</dependency>
 
+		<!-- GraphQL -->
+		<dependency>
+			<groupId>com.graphql-java</groupId>
+			<artifactId>graphql-java</artifactId>
+		</dependency>
+
 		<!-- SQL Builder -->
 		<dependency>
 			<groupId>com.healthmarketscience.sqlbuilder</groupId>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/JpaDstu3Config.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.config.dstu3;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigDstu3;
 import ca.uhn.fhir.jpa.config.JpaConfig;
@@ -9,6 +10,7 @@ import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
+import ca.uhn.fhir.jpa.graphql.GraphQLProviderWithIntrospection;
 import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.jpa.term.TermReadSvcDstu3;
 import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu3;
@@ -17,6 +19,7 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Meta;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@@ -62,8 +65,8 @@ public class JpaDstu3Config {
 
 	@Bean(name = JpaConfig.GRAPHQL_PROVIDER_NAME)
 	@Lazy
-	public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport) {
+	public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry, IDaoRegistry theDaoRegistry) {
-		return new GraphQLProvider(theFhirContext, theValidationSupport, theGraphqlStorageServices);
+		return new GraphQLProviderWithIntrospection(theFhirContext, theValidationSupport, theGraphqlStorageServices, theSearchParamRegistry, theDaoRegistry);
 	}
 
 	@Bean

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/JpaR4Config.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.config.r4;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR4;
 import ca.uhn.fhir.jpa.config.JpaConfig;
@@ -9,6 +10,7 @@ import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
+import ca.uhn.fhir.jpa.graphql.GraphQLProviderWithIntrospection;
 import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.jpa.term.TermReadSvcR4;
 import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcR4;
@@ -17,6 +19,7 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Meta;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@@ -26,6 +29,26 @@ import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+
 @Configuration
 @EnableTransactionManagement
 @Import({
@@ -48,8 +71,8 @@ public class JpaR4Config {
 
 	@Bean(name = JpaConfig.GRAPHQL_PROVIDER_NAME)
 	@Lazy
-	public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport) {
+	public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry, IDaoRegistry theDaoRegistry) {
-		return new GraphQLProvider(theFhirContext, theValidationSupport, theGraphqlStorageServices);
+        return new GraphQLProviderWithIntrospection(theFhirContext, theValidationSupport, theGraphqlStorageServices, theSearchParamRegistry, theDaoRegistry);
 	}
 
 	@Bean(name = "mySystemDaoR4")
@@ -77,23 +100,3 @@ public class JpaR4Config {
 	}
 
 }
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2022 Smile CDR, Inc.
- * %%
- * 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%
- */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/JpaR5Config.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.config.r5;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR5;
 import ca.uhn.fhir.jpa.config.JpaConfig;
@@ -9,6 +10,7 @@ import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
 import ca.uhn.fhir.jpa.dao.r5.TransactionProcessorVersionAdapterR5;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
+import ca.uhn.fhir.jpa.graphql.GraphQLProviderWithIntrospection;
 import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.jpa.term.TermReadSvcR5;
 import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcR5;
@@ -17,6 +19,7 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Meta;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@@ -68,8 +71,8 @@ public class JpaR5Config {
 
 	@Bean(name = JpaConfig.GRAPHQL_PROVIDER_NAME)
 	@Lazy
-	public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport) {
+	public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry, IDaoRegistry theDaoRegistry) {
-		return new GraphQLProvider(theFhirContext, theValidationSupport, theGraphqlStorageServices);
+        return new GraphQLProviderWithIntrospection(theFhirContext, theValidationSupport, theGraphqlStorageServices, theSearchParamRegistry, theDaoRegistry);
 	}
 
 	@Bean(name = "mySystemDaoR5")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java

@@ -161,6 +161,9 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
 	@Nullable
 	@Override
 	public <T extends IBaseResource> List<T> fetchAllStructureDefinitions() {
+		if (!myDaoRegistry.isResourceTypeSupported("StructureDefinition")) {
+			return null;
+		}
 		IBundleProvider search = myDaoRegistry.getResourceDao("StructureDefinition").search(new SearchParameterMap().setLoadSynchronousUpTo(1000));
 		return (List<T>) search.getResources(0, 1000);
 	}

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

@@ -0,0 +1,269 @@
+package ca.uhn.fhir.jpa.graphql;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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.FhirContext;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
+import ca.uhn.fhir.util.StringUtil;
+import ca.uhn.fhir.util.VersionUtil;
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import graphql.ExecutionResult;
+import graphql.GraphQL;
+import graphql.scalar.GraphqlStringCoercing;
+import graphql.schema.GraphQLScalarType;
+import graphql.schema.GraphQLSchema;
+import graphql.schema.idl.RuntimeWiring;
+import graphql.schema.idl.SchemaGenerator;
+import graphql.schema.idl.SchemaParser;
+import graphql.schema.idl.TypeDefinitionRegistry;
+import org.apache.commons.io.output.StringBuilderWriter;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContextWrapper;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r5.model.Enumerations;
+import org.hl7.fhir.r5.model.SearchParameter;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.utils.GraphQLSchemaGenerator;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
+import org.jetbrains.annotations.Nullable;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnull;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import static ca.uhn.fhir.util.MessageSupplier.msg;
+
+public class GraphQLProviderWithIntrospection extends GraphQLProvider {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(GraphQLProviderWithIntrospection.class);
+	private final GraphQLSchemaGenerator myGenerator;
+	private final ISearchParamRegistry mySearchParamRegistry;
+	private final VersionSpecificWorkerContextWrapper myContext;
+	private final IDaoRegistry myDaoRegistry;
+
+	/**
+	 * Constructor
+	 */
+	public GraphQLProviderWithIntrospection(FhirContext theFhirContext, IValidationSupport theValidationSupport, IGraphQLStorageServices theIGraphQLStorageServices, ISearchParamRegistry theSearchParamRegistry, IDaoRegistry theDaoRegistry) {
+		super(theFhirContext, theValidationSupport, theIGraphQLStorageServices);
+
+		mySearchParamRegistry = theSearchParamRegistry;
+		myDaoRegistry = theDaoRegistry;
+
+		myContext = VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(theValidationSupport);
+		myGenerator = new GraphQLSchemaGenerator(myContext, VersionUtil.getVersion());
+	}
+
+	@Override
+	public String processGraphQlGetRequest(ServletRequestDetails theRequestDetails, IIdType theId, String theQueryUrl) {
+		return super.processGraphQlGetRequest(theRequestDetails, theId, theQueryUrl);
+	}
+
+	@Override
+	public String processGraphQlPostRequest(ServletRequestDetails theServletRequestDetails, RequestDetails theRequestDetails, IIdType theId, String theQueryBody) {
+		if (theQueryBody.contains("__schema")) {
+			EnumSet<GraphQLSchemaGenerator.FHIROperationType> operations;
+			if (theId != null) {
+				throw new InvalidRequestException(Msg.code(2035) + "GraphQL introspection not supported at instance level. Please try at server- or instance- level.");
+			}
+
+			operations = EnumSet.of(GraphQLSchemaGenerator.FHIROperationType.READ, GraphQLSchemaGenerator.FHIROperationType.SEARCH);
+
+			Collection<String> resourceTypes;
+			if (theRequestDetails.getResourceName() != null) {
+				resourceTypes = Collections.singleton(theRequestDetails.getResourceName());
+			} else {
+				resourceTypes = new HashSet<>();
+				for (String next : myContext.getResourceNames()) {
+					if (myDaoRegistry.isResourceTypeSupported(next)) {
+						resourceTypes.add(next);
+					}
+				}
+				resourceTypes = resourceTypes
+					.stream()
+					.sorted()
+					.collect(Collectors.toList());
+			}
+
+			return generateSchema(theQueryBody, resourceTypes, operations);
+		} else {
+			return super.processGraphQlPostRequest(theServletRequestDetails, theRequestDetails, theId, theQueryBody);
+		}
+	}
+
+	private String generateSchema(String theQueryBody, Collection<String> theResourceTypes, EnumSet<GraphQLSchemaGenerator.FHIROperationType> theOperations) {
+
+		final StringBuilder schemaBuilder = new StringBuilder();
+		try (Writer writer = new StringBuilderWriter(schemaBuilder)) {
+			// Generate FHIR base types schemas
+			myGenerator.generateTypes(writer, theOperations);
+
+			// Fix up a few things that are missing from the generated schema
+			writer
+				.append("\ntype Resource {")
+				.append("\n  id: [token]" + "\n}")
+				.append("\n");
+			writer
+				.append("\ninput ResourceInput {")
+				.append("\n  id: [token]" + "\n}")
+				.append("\n");
+
+			// Generate schemas for the resource types
+			for (String nextResourceType : theResourceTypes) {
+				StructureDefinition sd = fetchStructureDefinition(nextResourceType);
+				List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry.getActiveSearchParams(nextResourceType).values());
+				myGenerator.generateResource(writer, sd, parameters, theOperations);
+			}
+
+			// Generate queries
+			writer.append("\ntype Query {");
+			for (String nextResourceType : theResourceTypes) {
+				if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.READ)) {
+					writer
+						.append("\n  ")
+						.append(nextResourceType)
+						.append("(id: String): ")
+						.append(nextResourceType)
+						.append("\n");
+				}
+				if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.SEARCH)) {
+					List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry.getActiveSearchParams(nextResourceType).values());
+					myGenerator.generateListAccessQuery(writer, parameters, nextResourceType);
+					myGenerator.generateConnectionAccessQuery(writer, parameters, nextResourceType);
+				}
+			}
+			writer.append("\n}");
+
+			writer.flush();
+		} catch (IOException e) {
+			throw new InternalErrorException(Msg.code(2036) + e.getMessage(), e);
+		}
+
+		String schema = schemaBuilder.toString().replace("\r", "");
+
+		// Set these to INFO if you're testing, then set back before committing
+		ourLog.debug("Schema generated: {} chars", schema.length());
+		ourLog.debug("Schema generated: {}", msg(() -> StringUtil.prependLineNumbers(schema)));
+
+		SchemaParser schemaParser = new SchemaParser();
+		TypeDefinitionRegistry typeDefinitionRegistry = schemaParser.parse(schema);
+
+		SchemaGenerator schemaGenerator = new SchemaGenerator();
+		RuntimeWiring.Builder runtimeWiringBuilder = RuntimeWiring.newRuntimeWiring();
+		for (String next : typeDefinitionRegistry.scalars().keySet()) {
+			if (Character.isUpperCase(next.charAt(0))) {
+				// Skip GraphQL built-in types
+				continue;
+			}
+			runtimeWiringBuilder.scalar(new GraphQLScalarType.Builder().name(next).coercing(new GraphqlStringCoercing()).build());
+		}
+
+		RuntimeWiring runtimeWiring = runtimeWiringBuilder.build();
+		GraphQLSchema graphQLSchema = schemaGenerator.makeExecutableSchema(typeDefinitionRegistry, runtimeWiring);
+
+		GraphQL build = GraphQL.newGraphQL(graphQLSchema).build();
+		ExecutionResult executionResult = build.execute(theQueryBody);
+
+		Map<String, Object> data = executionResult.toSpecification();
+		Gson gson = new GsonBuilder().create();
+		return gson.toJson(data);
+
+	}
+
+	@Nonnull
+	private List<SearchParameter> toR5SearchParams(Collection<RuntimeSearchParam> searchParams) {
+		List<SearchParameter> parameters = new ArrayList<>();
+		for (RuntimeSearchParam next : searchParams) {
+			SearchParameter sp = toR5SearchParam(next);
+			if (sp != null) {
+				parameters.add(sp);
+			}
+		}
+		return parameters;
+	}
+
+	@Nullable
+	private SearchParameter toR5SearchParam(RuntimeSearchParam next) {
+		SearchParameter sp = new SearchParameter();
+		sp.setUrl(next.getUri());
+		sp.setCode(next.getName());
+		sp.setName(next.getName());
+
+		switch (next.getParamType()) {
+			case NUMBER:
+				sp.setType(Enumerations.SearchParamType.NUMBER);
+				break;
+			case DATE:
+				sp.setType(Enumerations.SearchParamType.DATE);
+				break;
+			case STRING:
+				sp.setType(Enumerations.SearchParamType.STRING);
+				break;
+			case TOKEN:
+				sp.setType(Enumerations.SearchParamType.TOKEN);
+				break;
+			case REFERENCE:
+				sp.setType(Enumerations.SearchParamType.REFERENCE);
+				break;
+			case COMPOSITE:
+				sp.setType(Enumerations.SearchParamType.COMPOSITE);
+				break;
+			case QUANTITY:
+				sp.setType(Enumerations.SearchParamType.QUANTITY);
+				break;
+			case URI:
+				sp.setType(Enumerations.SearchParamType.URI);
+				break;
+			case HAS:
+			case SPECIAL:
+			default:
+				return null;
+		}
+		return sp;
+	}
+
+	@Nonnull
+	private StructureDefinition fetchStructureDefinition(String resourceName) {
+		StructureDefinition retVal = myContext.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName);
+		Validate.notNull(retVal);
+		return retVal;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java

@@ -722,16 +722,6 @@ public abstract class BaseJpaTest extends BaseTest {
 		doRandomizeLocaleAndTimezone();
 	}
 
-	@AfterAll
-	public static void afterClassShutdownDerby() {
-		// DriverManager.getConnection("jdbc:derby:;shutdown=true");
-		// try {
-		// DriverManager.getConnection("jdbc:derby:memory:myUnitTestDB;drop=true");
-		// } catch (SQLNonTransientConnectionException e) {
-		// // expected.. for some reason....
-		// }
-	}
-
 	public static String loadClasspath(String resource) throws IOException {
 		return new String(loadClasspathBytes(resource), Constants.CHARSET_UTF8);
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -17,6 +17,7 @@ import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.QuantityParam;
+import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -105,6 +106,10 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 				.collect(Collectors.toList());
 			assertThat(paths.toString(), paths, contains("Observation.subject", "Observation.subject.where(resolve() is Patient)"));
 		});
+
+		myCaptureQueriesListener.clear();
+		assertEquals(1, myObservationDao.search(SearchParameterMap.newSynchronous("patient", new ReferenceParam("Patient/A"))).sizeOrThrowNpe());
+		myCaptureQueriesListener.logSelectQueries();
 	}
 
 	@Test

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

@@ -5,12 +5,9 @@ import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
 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.server.RestfulServerExtension;
-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;
@@ -19,9 +16,6 @@ import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
-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;
@@ -35,6 +29,7 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
 
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
@@ -47,15 +42,19 @@ import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-public class JpaGraphQLR4ProviderTest {
+public class GraphQLR4ProviderTest {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaGraphQLR4ProviderTest.class);
 	public static final String DATA_PREFIX = "{\"data\": ";
 	public static final String DATA_SUFFIX = "}";
-	private static CloseableHttpClient ourClient;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GraphQLR4ProviderTest.class);
 	private static final FhirContext ourCtx = FhirContext.forR4Cached();
-	private static int ourPort;
+	private static CloseableHttpClient ourClient;
-	private static Server ourServer;
+	private MyStorageServices myGraphQLStorageServices = new MyStorageServices();
+
+	@RegisterExtension
+	private RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(ourCtx)
+		.registerProvider(new DummyPatientResourceProvider())
+		.registerProvider(new GraphQLProvider(myGraphQLStorageServices));
 
 	@BeforeEach
 	public void before() {
@@ -65,9 +64,8 @@ public class JpaGraphQLR4ProviderTest {
 	@Test
 	public void testGraphInstance() throws Exception {
 		String query = "{name{family,given}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/Patient/123/$graphql?query=" + UrlUtil.escapeUrlParam(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -81,9 +79,6 @@ public class JpaGraphQLR4ProviderTest {
 				"  }]\n" +
 				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
@@ -91,9 +86,8 @@ public class JpaGraphQLR4ProviderTest {
 	@Test
 	public void testGraphInstanceWithFhirpath() throws Exception {
 		String query = "{name(fhirpath:\"family.exists()\"){text,given,family}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/Patient/123/$graphql?query=" + UrlUtil.escapeUrlParam(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -105,9 +99,6 @@ public class JpaGraphQLR4ProviderTest {
 				"  }]\n" +
 				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
@@ -115,9 +106,8 @@ public class JpaGraphQLR4ProviderTest {
 	@Test
 	public void testGraphSystemInstance() throws Exception {
 		String query = "{Patient(id:123){id,name{given,family}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -133,9 +123,6 @@ public class JpaGraphQLR4ProviderTest {
 				"  }\n" +
 				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
@@ -143,9 +130,9 @@ public class JpaGraphQLR4ProviderTest {
 	@Test
 	public void testGraphSystemList() throws Exception {
 		String query = "{PatientList(name:\"pet\"){name{family,given}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+
-		try {
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -166,8 +153,6 @@ public class JpaGraphQLR4ProviderTest {
 				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
 
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
@@ -175,9 +160,8 @@ public class JpaGraphQLR4ProviderTest {
 	@Test
 	public void testGraphSystemArrayArgumentList() throws Exception {
 		String query = "{PatientList(id:[\"hapi-123\",\"hapi-124\"]){id,name{family}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
@@ -196,41 +180,21 @@ public class JpaGraphQLR4ProviderTest {
 				"  }]\n" +
 				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
 
 	@AfterAll
 	public static void afterClassClearContext() throws Exception {
-		JettyUtil.closeServer(ourServer);
+		ourClient.close();
 	}
 
 	@BeforeAll
 	public static void beforeClass() throws Exception {
-		ourServer = new Server(0);
-
-		ServletHandler proxyHandler = new ServletHandler();
-		RestfulServer servlet = new RestfulServer(ourCtx);
-		servlet.setDefaultResponseEncoding(EncodingEnum.JSON);
-		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
-
-		servlet.registerProvider(new DummyPatientResourceProvider());
-		MyStorageServices storageServices = new MyStorageServices();
-		servlet.registerProvider(new GraphQLProvider(storageServices));
-		ServletHolder servletHolder = new ServletHolder(servlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		ourServer.setHandler(proxyHandler);
-		JettyUtil.startServer(ourServer);
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
-
 		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
 		HttpClientBuilder builder = HttpClientBuilder.create();
 		builder.setConnectionManager(connectionManager);
 		ourClient = builder.build();
-
 	}
 
 	public static class DummyPatientResourceProvider implements IResourceProvider {

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

@@ -14,8 +14,8 @@ import org.slf4j.LoggerFactory;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 
-import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_PREFIX;
+import static ca.uhn.fhir.jpa.provider.GraphQLR4ProviderTest.DATA_PREFIX;
-import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_SUFFIX;
+import static ca.uhn.fhir.jpa.provider.GraphQLR4ProviderTest.DATA_SUFFIX;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {

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

@@ -1,93 +0,0 @@
-package ca.uhn.fhir.jpa.provider.r4;
-
-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.r4.model.Patient;
-import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-import java.nio.charset.StandardCharsets;
-
-import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_PREFIX;
-import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_SUFFIX;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
-	private Logger ourLog = LoggerFactory.getLogger(GraphQLProviderR4Test.class);
-	private IIdType myPatientId0;
-
-	@Test
-	public void testInstanceSimpleRead() throws IOException {
-		initTestPatients();
-
-		String query = "{name{family,given}}";
-		HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
-
-		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
-			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(resp);
-			assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
-				"  \"name\":[{\n" +
-				"    \"family\":\"FAM\",\n" +
-				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
-				"  },{\n" +
-				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
-				"  }]\n" +
-				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
-		}
-
-	}
-
-	@Test
-	public void testSystemSimpleSearch() throws IOException {
-		initTestPatients();
-
-		String query = "{PatientList(given:\"given\"){name{family,given}}}";
-		HttpGet httpGet = new HttpGet(ourServerBase + "/$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.stripWhitespace(DATA_PREFIX + "{\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" +
-				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
-		}
-	}
-
-	private void initTestPatients() {
-		Patient p = new Patient();
-		p.addName()
-			.setFamily("FAM")
-			.addGiven("GIVEN1")
-			.addGiven("GIVEN2");
-		p.addName()
-			.addGiven("GivenOnly1")
-			.addGiven("GivenOnly2");
-		myPatientId0 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addName()
-			.addGiven("GivenOnlyB1")
-			.addGiven("GivenOnlyB2");
-		myClient.create().resource(p).execute();
-	}
-
-
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLR4Test.java

@@ -0,0 +1,227 @@
+package ca.uhn.fhir.jpa.provider.r4;
+
+import ca.uhn.fhir.util.FileUtil;
+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.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestMethodOrder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+
+import static ca.uhn.fhir.jpa.provider.GraphQLR4ProviderTest.DATA_PREFIX;
+import static ca.uhn.fhir.jpa.provider.GraphQLR4ProviderTest.DATA_SUFFIX;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+@TestMethodOrder(MethodOrderer.MethodName.class)
+public class GraphQLR4Test extends BaseResourceProviderR4Test {
+	public static final String INTROSPECTION_QUERY = "{\"query\":\"\\n    query IntrospectionQuery {\\n      __schema {\\n        queryType { name }\\n        mutationType { name }\\n        subscriptionType { name }\\n        types {\\n          ...FullType\\n        }\\n        directives {\\n          name\\n          description\\n          locations\\n          args {\\n            ...InputValue\\n          }\\n        }\\n      }\\n    }\\n\\n    fragment FullType on __Type {\\n      kind\\n      name\\n      description\\n      fields(includeDeprecated: true) {\\n        name\\n        description\\n        args {\\n          ...InputValue\\n        }\\n        type {\\n          ...TypeRef\\n        }\\n        isDeprecated\\n        deprecationReason\\n      }\\n      inputFields {\\n        ...InputValue\\n      }\\n      interfaces {\\n        ...TypeRef\\n      }\\n      enumValues(includeDeprecated: true) {\\n        name\\n        description\\n        isDeprecated\\n        deprecationReason\\n      }\\n      possibleTypes {\\n        ...TypeRef\\n      }\\n    }\\n\\n    fragment InputValue on __InputValue {\\n      name\\n      description\\n      type { ...TypeRef }\\n      defaultValue\\n    }\\n\\n    fragment TypeRef on __Type {\\n      kind\\n      name\\n      ofType {\\n        kind\\n        name\\n        ofType {\\n          kind\\n          name\\n          ofType {\\n            kind\\n            name\\n            ofType {\\n              kind\\n              name\\n              ofType {\\n                kind\\n                name\\n                ofType {\\n                  kind\\n                  name\\n                  ofType {\\n                    kind\\n                    name\\n                  }\\n                }\\n              }\\n            }\\n          }\\n        }\\n      }\\n    }\\n  \",\"operationName\":\"IntrospectionQuery\"}";
+	private Logger ourLog = LoggerFactory.getLogger(GraphQLR4Test.class);
+	private IIdType myPatientId0;
+
+	@Test
+	public void testInstance_Read_Patient() throws IOException {
+		initTestPatients();
+
+		String query = "{name{family,given}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
+				"  \"name\":[{\n" +
+				"    \"family\":\"FAM\",\n" +
+				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"  },{\n" +
+				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"  }]\n" +
+				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
+		}
+
+	}
+
+	@Test
+	public void testType_Introspect_Patient() throws IOException {
+		initTestPatients();
+
+		String uri = ourServerBase + "/Patient/$graphql";
+		HttpPost httpGet = new HttpPost(uri);
+		httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON));
+
+		// Repeat a couple of times to make sure it doesn't fail after the first one. At one point
+		// the generator polluted the structure userdata and failed the second time
+		for (int i = 0; i < 3; i++) {
+			try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+				String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+				ourLog.info(resp);
+				assertEquals(200, response.getStatusLine().getStatusCode());
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\","));
+				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\",")));
+				assertThat(resp, not(containsString("\"name\":\"Observation\",\"args\":[{\"name\":\"id\"")));
+				assertThat(resp, not(containsString("\"name\":\"ObservationList\",\"args\":[{\"name\":\"_filter\"")));
+				assertThat(resp, not(containsString("\"name\":\"ObservationConnection\",\"fields\":[{\"name\":\"count\"")));
+				assertThat(resp, containsString("\"name\":\"Patient\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"PatientList\",\"args\":[{\"name\":\"_filter\""));
+			}
+		}
+	}
+
+	@Test
+	public void testType_Introspect_Observation() throws IOException {
+		initTestPatients();
+
+		String uri = ourServerBase + "/Observation/$graphql";
+		HttpPost httpGet = new HttpPost(uri);
+		httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON));
+
+		// Repeat a couple of times to make sure it doesn't fail after the first one. At one point
+		// the generator polluted the structure userdata and failed the second time
+		for (int i = 0; i < 3; i++) {
+			try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+				String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+				ourLog.info(resp);
+				assertEquals(200, response.getStatusLine().getStatusCode());
+				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\",")));
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\","));
+				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"PatientList\"")));
+				assertThat(resp, containsString("\"name\":\"Observation\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"ObservationList\",\"args\":[{\"name\":\"_filter\""));
+				assertThat(resp, containsString("\"name\":\"ObservationConnection\",\"fields\":[{\"name\":\"count\""));
+				assertThat(resp, not(containsString("\"name\":\"Patient\",\"args\":[{\"name\":\"id\"")));
+				assertThat(resp, not(containsString("\"name\":\"PatientList\",\"args\":[{\"name\":\"_filter\"")));
+			}
+		}
+	}
+
+	@Test
+	public void testRoot_Introspect() throws IOException {
+		initTestPatients();
+
+		String uri = ourServerBase + "/$graphql";
+		HttpPost httpGet = new HttpPost(uri);
+		httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON));
+
+		// Repeat a couple of times to make sure it doesn't fail after the first one. At one point
+		// the generator polluted the structure userdata and failed the second time
+		for (int i = 0; i < 3; i++) {
+			try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+				String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+				ourLog.info("Response has size: {}", FileUtil.formatFileSize(resp.length()));
+				assertEquals(200, response.getStatusLine().getStatusCode());
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\","));
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\","));
+				assertThat(resp, containsString("\"name\":\"Observation\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"ObservationList\",\"args\":[{\"name\":\"_filter\""));
+				assertThat(resp, containsString("\"name\":\"ObservationConnection\",\"fields\":[{\"name\":\"count\""));
+				assertThat(resp, containsString("\"name\":\"Patient\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"PatientList\",\"args\":[{\"name\":\"_filter\""));
+			}
+		}
+	}
+
+	@Test
+	public void testRoot_Read_Patient() throws IOException {
+		initTestPatients();
+
+		String query = "{Patient(id:\"" + myPatientId0.getIdPart() + "\"){name{family,given}}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(TestUtil.stripWhitespace(DATA_PREFIX +
+				"{\n" +
+				"\"Patient\":{\n" +
+				"\"name\":[{\n" +
+				"\"family\":\"FAM\",\n" +
+				"\"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"},{\n" +
+				"\"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"}]\n" +
+				"}\n" +
+				"}" +
+				DATA_SUFFIX), TestUtil.stripWhitespace(resp));
+		}
+
+	}
+
+
+
+	@Test
+	public void testRoot_Search_Patient() throws IOException {
+		initTestPatients();
+
+		String query = "{PatientList(given:\"given\"){name{family,given}}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/$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.stripWhitespace(DATA_PREFIX + "{\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" +
+				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
+		}
+
+	}
+
+	@Test
+	public void testRoot_Search_Observation() throws IOException {
+		initTestPatients();
+
+		String query = "{ObservationList(date: \"2022\") {id}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+
+		myCaptureQueriesListener.clear();
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+		}
+		myCaptureQueriesListener.logSelectQueries();
+	}
+
+	private void initTestPatients() {
+		Patient p = new Patient();
+		p.addName()
+			.setFamily("FAM")
+			.addGiven("GIVEN1")
+			.addGiven("GIVEN2");
+		p.addName()
+			.addGiven("GivenOnly1")
+			.addGiven("GivenOnly2");
+		myPatientId0 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addName()
+			.addGiven("GivenOnlyB1")
+			.addGiven("GivenOnlyB2");
+		myClient.create().resource(p).execute();
+	}
+
+
+}

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -19,6 +19,7 @@
 			<groupId>org.postgresql</groupId>
 			<artifactId>postgresql</artifactId>
 		</dependency>
+
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
@@ -102,6 +103,12 @@
 		</dependency>
 
 		<!-- TEST DEPS -->
+		<dependency>
+			<groupId>com.h2database</groupId>
+			<artifactId>h2</artifactId>
+			<scope>test</scope>
+		</dependency>
+
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-servlets</artifactId>

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

@@ -35,6 +35,7 @@ import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+import ca.uhn.fhirtest.config.SqlCaptureInterceptor;
 import ca.uhn.fhirtest.config.TestDstu2Config;
 import ca.uhn.fhirtest.config.TestDstu3Config;
 import ca.uhn.fhirtest.config.TestR4Config;
@@ -282,6 +283,8 @@ public class TestRestfulServer extends RestfulServer {
 		loggingInterceptor.setMessageFormat("${operationType} Content-Type: ${requestHeader.content-type} - Accept: ${responseEncodingNoDefault} \"${requestHeader.accept}\" - Agent: ${requestHeader.user-agent}");
 		registerInterceptor(loggingInterceptor);
 
+		// SQL Capturing
+		registerInterceptor(myAppCtx.getBean(SqlCaptureInterceptor.class));
 	}
 
 	/**

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -5,11 +5,11 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.HapiJpaConfig;
 import ca.uhn.fhir.jpa.config.JpaDstu2Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.IValidatorModule;
@@ -22,7 +22,6 @@ import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -44,16 +43,11 @@ import java.util.concurrent.TimeUnit;
 @EnableTransactionManagement()
 public class TestDstu2Config {
 
-	public static final String FHIR_LUCENE_LOCATION_DSTU2 = "${fhir.lucene.location.dstu2}";
+	public static final String FHIR_LUCENE_LOCATION_DSTU2 = "fhir.lucene.location.dstu2";
 
-	@Value(TestDstu3Config.FHIR_DB_USERNAME)
+	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);
-	private String myDbUsername;
+	private String myDbPassword = System.getProperty(TestR5Config.FHIR_DB_PASSWORD);
-
+	private String myFhirLuceneLocation = System.getProperty(FHIR_LUCENE_LOCATION_DSTU2);
-	@Value(TestDstu3Config.FHIR_DB_PASSWORD)
-	private String myDbPassword;
-
-	@Value(FHIR_LUCENE_LOCATION_DSTU2)
-	private String myFhirLuceneLocation;
 
 	@Bean
 	public PublicSecurityInterceptor securityInterceptor() {
@@ -88,7 +82,9 @@ public class TestDstu2Config {
 
 	@Bean
 	public ModelConfig modelConfig() {
-		return daoConfig().getModelConfig();
+		ModelConfig retVal = daoConfig().getModelConfig();
+		retVal.setIndexIdentifierOfType(true);
+		return retVal;
 	}
 
 	@Bean
@@ -103,7 +99,7 @@ public class TestDstu2Config {
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_dstu2;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_dstu2");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_dstu2");
@@ -144,7 +140,7 @@ public class TestDstu2Config {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}
@@ -168,6 +164,7 @@ public class TestDstu2Config {
 
 	/**
 	 * Bean which validates incoming requests
+	 *
 	 * @param theInstanceValidator
 	 */
 	@Bean

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -5,12 +5,12 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.HapiJpaConfig;
 import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
@@ -23,7 +23,6 @@ import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -48,14 +47,9 @@ public class TestDstu3Config {
 	public static final String FHIR_DB_PASSWORD = "${fhir.db.password}";
 	public static final String FHIR_LUCENE_LOCATION_DSTU3 = "${fhir.lucene.location.dstu3}";
 
-	@Value(TestDstu3Config.FHIR_DB_USERNAME)
+	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);
-	private String myDbUsername;
+	private String myDbPassword = System.getProperty(TestR5Config.FHIR_DB_PASSWORD);
-
+	private String myFhirLuceneLocation = System.getProperty(FHIR_LUCENE_LOCATION_DSTU3);
-	@Value(TestDstu3Config.FHIR_DB_PASSWORD)
-	private String myDbPassword;
-
-	@Value(FHIR_LUCENE_LOCATION_DSTU3)
-	private String myFhirLuceneLocation;
 
 	@Bean
 	public DaoConfig daoConfig() {
@@ -85,7 +79,9 @@ public class TestDstu3Config {
 
 	@Bean
 	public ModelConfig modelConfig() {
-		return daoConfig().getModelConfig();
+		ModelConfig retVal = daoConfig().getModelConfig();
+		retVal.setIndexIdentifierOfType(true);
+		return retVal;
 	}
 
 
@@ -114,7 +110,7 @@ public class TestDstu3Config {
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_dstu3;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_dstu3");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_dstu3");
@@ -147,7 +143,7 @@ public class TestDstu3Config {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}
@@ -171,6 +167,7 @@ public class TestDstu3Config {
 
 	/**
 	 * Bean which validates incoming requests
+	 *
 	 * @param theFhirInstanceValidator
 	 */
 	@Bean

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -5,12 +5,12 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.HapiJpaConfig;
 import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
@@ -23,7 +23,6 @@ import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -49,14 +48,9 @@ public class TestR4Config {
 	public static final String FHIR_LUCENE_LOCATION_R4 = "${fhir.lucene.location.r4}";
 	public static final Integer COUNT_SEARCH_RESULTS_UP_TO = 50000;
 
-	@Value(TestR4Config.FHIR_DB_USERNAME)
+	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);
-	private String myDbUsername;
+	private String myDbPassword = System.getProperty(TestR5Config.FHIR_DB_PASSWORD);
-
+	private String myFhirLuceneLocation = System.getProperty(FHIR_LUCENE_LOCATION_R4);
-	@Value(TestR4Config.FHIR_DB_PASSWORD)
-	private String myDbPassword;
-
-	@Value(FHIR_LUCENE_LOCATION_R4)
-	private String myFhirLuceneLocation;
 
 	@Bean
 	public DaoConfig daoConfig() {
@@ -85,7 +79,9 @@ public class TestR4Config {
 
 	@Bean
 	public ModelConfig modelConfig() {
-		return daoConfig().getModelConfig();
+		ModelConfig retVal = daoConfig().getModelConfig();
+		retVal.setIndexIdentifierOfType(true);
+		return retVal;
 	}
 
 
@@ -101,7 +97,7 @@ public class TestR4Config {
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_r4;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_r4");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_r4");
@@ -142,7 +138,7 @@ public class TestR4Config {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}
@@ -165,6 +161,7 @@ public class TestR4Config {
 
 	/**
 	 * Bean which validates incoming requests
+	 *
 	 * @param theFhirInstanceValidator
 	 */
 	@Bean
@@ -202,5 +199,4 @@ public class TestR4Config {
 	}
 
 
-
 }

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -5,12 +5,12 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.HapiJpaConfig;
 import ca.uhn.fhir.jpa.config.r5.JpaR5Config;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.IInstanceValidatorModule;
@@ -23,7 +23,8 @@ import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
-import org.springframework.beans.factory.annotation.Value;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -48,15 +49,10 @@ public class TestR5Config {
 	public static final String FHIR_DB_PASSWORD = "${fhir.db.password}";
 	public static final String FHIR_LUCENE_LOCATION_R5 = "${fhir.lucene.location.r5}";
 	public static final Integer COUNT_SEARCH_RESULTS_UP_TO = 50000;
-
+	private static final Logger ourLog = LoggerFactory.getLogger(TestR5Config.class);
-	@Value(TestR5Config.FHIR_DB_USERNAME)
+	private String myDbUsername = System.getProperty(TestR5Config.FHIR_DB_USERNAME);
-	private String myDbUsername;
+	private String myDbPassword = System.getProperty(TestR5Config.FHIR_DB_PASSWORD);
-
+	private String myFhirLuceneLocation = System.getProperty(FHIR_LUCENE_LOCATION_R5);
-	@Value(TestR5Config.FHIR_DB_PASSWORD)
-	private String myDbPassword;
-
-	@Value(FHIR_LUCENE_LOCATION_R5)
-	private String myFhirLuceneLocation;
 
 	@Bean
 	public DaoConfig daoConfig() {
@@ -85,7 +81,9 @@ public class TestR5Config {
 
 	@Bean
 	public ModelConfig modelConfig() {
-		return daoConfig().getModelConfig();
+		ModelConfig retVal = daoConfig().getModelConfig();
+		retVal.setIndexIdentifierOfType(true);
+		return retVal;
 	}
 
 	@Bean
@@ -97,9 +95,12 @@ public class TestR5Config {
 
 	@Bean(name = "myPersistenceDataSourceR5")
 	public DataSource dataSource() {
+		ourLog.info("Starting R5 database with DB username: {}", myDbUsername);
+		ourLog.info("Have system property username: {}", System.getProperty(FHIR_DB_USERNAME));
+
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_r5;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_r5");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_r5");
@@ -141,7 +142,7 @@ public class TestR5Config {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}
@@ -165,6 +166,7 @@ public class TestR5Config {
 
 	/**
 	 * Bean which validates incoming requests
+	 *
 	 * @param theFhirInstanceValidator
 	 */
 	@Bean
@@ -202,5 +204,4 @@ public class TestR5Config {
 	}
 
 
-
 }

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProvider.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.rest.annotation.GraphQL;
@@ -32,6 +33,7 @@ import ca.uhn.fhir.rest.annotation.GraphQLQueryUrl;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Initialize;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -39,12 +41,12 @@ 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 ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 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.Package;
 import org.hl7.fhir.utilities.graphql.Parser;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -54,9 +56,10 @@ import javax.annotation.Nullable;
 import java.util.function.Supplier;
 
 public class GraphQLProvider {
-	private final Supplier<IGraphQLEngine> engineFactory;
+	private static final Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
+
+	private final Supplier<IGraphQLEngine> myEngineFactory;
 	private final IGraphQLStorageServices myStorageServices;
-	private Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
 
 	/**
 	 * Constructor which uses a default context and validation support object
@@ -83,21 +86,21 @@ public class GraphQLProvider {
 				IValidationSupport validationSupport = theValidationSupport;
 				validationSupport = ObjectUtils.defaultIfNull(validationSupport, new DefaultProfileValidationSupport(theFhirContext));
 				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);
+				myEngineFactory = () -> new org.hl7.fhir.dstu3.utils.GraphQLEngine(workerContext);
 				break;
 			}
 			case R4: {
 				IValidationSupport validationSupport = theValidationSupport;
 				validationSupport = ObjectUtils.defaultIfNull(validationSupport, new DefaultProfileValidationSupport(theFhirContext));
 				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);
+				myEngineFactory = () -> new org.hl7.fhir.r4.utils.GraphQLEngine(workerContext);
 				break;
 			}
 			case R5: {
 				IValidationSupport validationSupport = theValidationSupport;
 				validationSupport = ObjectUtils.defaultIfNull(validationSupport, new DefaultProfileValidationSupport(theFhirContext));
 				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);
+				myEngineFactory = () -> new org.hl7.fhir.r5.utils.GraphQLEngine(workerContext);
 				break;
 			}
 			case DSTU2:
@@ -111,8 +114,8 @@ public class GraphQLProvider {
 		myStorageServices = theStorageServices;
 	}
 
-	@Description(value="This operation invokes a GraphQL expression for fetching an joining a graph of resources, returning them in a custom format.")
+	@Description(value = "This operation invokes a GraphQL expression for fetching an joining a graph of resources, returning them in a custom format.")
-	@GraphQL(type=RequestTypeEnum.GET)
+	@GraphQL(type = RequestTypeEnum.GET)
 	public String processGraphQlGetRequest(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQueryUrl String theQueryUrl) {
 		if (theQueryUrl != null) {
 			return processGraphQLRequest(theRequestDetails, theId, theQueryUrl);
@@ -120,24 +123,31 @@ public class GraphQLProvider {
 		throw new InvalidRequestException(Msg.code(1144) + "Unable to parse empty GraphQL expression");
 	}
 
-	@Description(value="This operation invokes a GraphQL expression for fetching an joining a graph of resources, returning them in a custom format.")
+	@Description(value = "This operation invokes a GraphQL expression for fetching an joining a graph of resources, returning them in a custom format.")
-	@GraphQL(type=RequestTypeEnum.POST)
+	@GraphQL(type = RequestTypeEnum.POST)
-	public String processGraphQlPostRequest(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQueryBody String theQueryBody) {
+	public String processGraphQlPostRequest(ServletRequestDetails theServletRequestDetails, RequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQueryBody String theQueryBody) {
 		if (theQueryBody != null) {
-			return processGraphQLRequest(theRequestDetails, theId, theQueryBody);
+			return processGraphQLRequest(theServletRequestDetails, theId, theQueryBody);
 		}
 		throw new InvalidRequestException(Msg.code(1145) + "Unable to parse empty GraphQL expression");
 	}
 
 	public String processGraphQLRequest(ServletRequestDetails theRequestDetails, IIdType theId, String theQuery) {
-		IGraphQLEngine engine = engineFactory.get();
+		Package parsedGraphQLRequest;
+		try {
+			parsedGraphQLRequest = Parser.parse(theQuery);
+		} catch (Exception e) {
+			throw new InvalidRequestException(Msg.code(1146) + "Unable to parse GraphQL Expression: " + e);
+		}
+
+		return processGraphQLRequest(theRequestDetails, theId, parsedGraphQLRequest);
+	}
+
+	protected String processGraphQLRequest(ServletRequestDetails theRequestDetails, IIdType theId, Package parsedGraphQLRequest) {
+		IGraphQLEngine engine = myEngineFactory.get();
 		engine.setAppInfo(theRequestDetails);
 		engine.setServices(myStorageServices);
-		try {
+		engine.setGraphQL(parsedGraphQLRequest);
-			engine.setGraphQL(Parser.parse(theQuery));
-		} catch (Exception theE) {
-			throw new InvalidRequestException(Msg.code(1146) + "Unable to parse GraphQL Expression: " + theE.toString());
-		}
 
 		try {
 
@@ -167,7 +177,7 @@ public class GraphQLProvider {
 				ourLog.error("Failure during GraphQL processing", e);
 			}
 			b.append(e.getMessage());
-			throw new UnclassifiedServerFailureException(statusCode, Msg.code(1147) + b.toString());
+			throw new UnclassifiedServerFailureException(statusCode, Msg.code(1147) + b);
 		}
 	}
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/LoggingInterceptorTest.java

@@ -41,7 +41,7 @@ import static org.mockito.Mockito.when;
 
 public class LoggingInterceptorTest {
 
-	private static FhirContext ourCtx = FhirContext.forR4();
+	private static final FhirContext ourCtx = FhirContext.forR4Cached();
 	private static int ourPort;
 	private static Server ourServer;
 	private Logger myLoggerRoot;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/GraphQLR4RawTest.java

@@ -8,10 +8,10 @@ import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
 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.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
-import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.io.IOUtils;
@@ -22,9 +22,6 @@ import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.servlet.ServletHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.IdType;
@@ -33,10 +30,10 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
 
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.TimeUnit;
 
@@ -44,63 +41,37 @@ import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 
 public class GraphQLR4RawTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GraphQLR4RawTest.class);
 	private static CloseableHttpClient ourClient;
-	private static FhirContext ourCtx = FhirContext.forR4();
+	private static final FhirContext ourCtx = FhirContext.forR4Cached();
-	private static int ourPort;
-	private static Server ourServer;
 	private static String ourNextRetVal;
 	private static IdType ourLastId;
 	private static String ourLastQuery;
-	private static int ourMethodCount;
+	private static String ourLastResourceType;
 
-	@AfterAll
+	@RegisterExtension
-	public static void afterClassClearContext() throws Exception {
+	private final RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(ourCtx)
-		JettyUtil.closeServer(ourServer);
+		.registerProvider(new MyPatientResourceProvider())
-		TestUtil.randomizeLocaleAndTimezone();
+		.registerProvider(new MyGraphQLProvider());
-	}
-
-	@BeforeAll
-	public static void beforeClass() throws Exception {
-		ourServer = new Server(0);
-
-		ServletHandler proxyHandler = new ServletHandler();
-		RestfulServer servlet = new RestfulServer(ourCtx);
-		servlet.setDefaultResponseEncoding(EncodingEnum.JSON);
-		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
-
-		servlet.registerProviders(Collections.singletonList(new MyGraphQLProvider()));
-		servlet.registerProvider(new MyPatientResourceProvider());
-		ServletHolder servletHolder = new ServletHolder(servlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		ourServer.setHandler(proxyHandler);
-		JettyUtil.startServer(ourServer);
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
-
-		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
-		HttpClientBuilder builder = HttpClientBuilder.create();
-		builder.setConnectionManager(connectionManager);
-		ourClient = builder.build();
-
-	}
 
 	@BeforeEach
 	public void before() {
 		ourNextRetVal = null;
 		ourLastId = null;
 		ourLastQuery = null;
-		ourMethodCount = 0;
+		ourLastResourceType = null;
 	}
 
 	@Test
-	public void testGraphInstance() throws Exception {
+	public void testGraphInstance_Get() throws Exception {
 		ourNextRetVal = "{\"foo\"}";
 
 
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escapeUrlParam("{name{family,given}}"));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/Patient/123/$graphql?query=" + UrlUtil.escapeUrlParam("{name{family,given}}"));
 		CloseableHttpResponse status = ourClient.execute(httpGet);
 		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
@@ -118,12 +89,29 @@ public class GraphQLR4RawTest {
 
 	}
 
-
 	@Test
-	public void testGraphPostContentTypeJson() throws Exception {
+	public void testGraphInstance_Get_UnsupportedResourceType() throws Exception {
 		ourNextRetVal = "{\"foo\"}";
 
-		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/123/$graphql");
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/Condition/123/$graphql?query=" + UrlUtil.escapeUrlParam("{name{family,given}}"));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(404, status.getStatusLine().getStatusCode());
+			assertThat(responseContent, containsString("Unknown resource type"));
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testGraphInstance_Post_ContentTypeJson() throws Exception {
+		ourNextRetVal = "{\"foo\"}";
+
+		HttpPost httpPost = new HttpPost("http://localhost:" + myRestfulServerExtension.getPort() + "/Patient/123/$graphql");
 		StringEntity entity = new StringEntity("{\"query\": \"{name{family,given}}\"}");
 		httpPost.setEntity(entity);
 		httpPost.setHeader("Accept", "application/json");
@@ -147,10 +135,10 @@ public class GraphQLR4RawTest {
 	}
 
 	@Test
-	public void testGraphPostContentTypeGraphql() throws Exception {
+	public void testGraphInstance_Post_ContentTypeGraphql() throws Exception {
 		ourNextRetVal = "{\"foo\"}";
 
-		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/123/$graphql");
+		HttpPost httpPost = new HttpPost("http://localhost:" + myRestfulServerExtension.getPort() + "/Patient/123/$graphql");
 		StringEntity entity = new StringEntity("{name{family,given}}");
 		httpPost.setEntity(entity);
 		httpPost.setHeader("Accept", "application/json");
@@ -166,6 +154,7 @@ public class GraphQLR4RawTest {
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
 			assertEquals("Patient/123", ourLastId.getValue());
 			assertEquals("{name{family,given}}", ourLastQuery);
+			assertEquals("Patient", ourLastResourceType);
 
 		} finally {
 			IOUtils.closeQuietly(status.getEntity().getContent());
@@ -173,31 +162,41 @@ public class GraphQLR4RawTest {
 
 	}
 
-
 	@Test
-	public void testGraphInstanceUnknownType() throws Exception {
+	public void testGraphBase_Post_ListQuery() throws Exception {
 		ourNextRetVal = "{\"foo\"}";
 
+		HttpPost httpPost = new HttpPost("http://localhost:" + myRestfulServerExtension.getPort() + "/$graphql");
+		StringEntity entity = new StringEntity("{\"query\": \"{PatientList(date: \\\"2022\\\") {name{family,given}}}\"}");
+		httpPost.setEntity(entity);
+		httpPost.setHeader("Accept", "application/json");
+		httpPost.setHeader("Content-type", "application/json");
 
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Condition/123/$graphql?query=" + UrlUtil.escapeUrlParam("{name{family,given}}"));
+		CloseableHttpResponse status = ourClient.execute(httpPost);
-		CloseableHttpResponse status = ourClient.execute(httpGet);
 		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
-			assertEquals(404, status.getStatusLine().getStatusCode());
+			assertEquals(200, status.getStatusLine().getStatusCode());
-			assertThat(responseContent, containsString("Unknown resource type"));
+
+			assertEquals("{\"foo\"}", responseContent);
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
+			assertNull(ourLastId);
+			assertNull(ourLastResourceType);
+			assertEquals("{PatientList(date: \"2022\") {name{family,given}}}", ourLastQuery);
+
 		} finally {
 			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
 
+
 	@Test
 	public void testGraphSystem() throws Exception {
 		ourNextRetVal = "{\"foo\"}";
 
 
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escapeUrlParam("{name{family,given}}"));
+		HttpGet httpGet = new HttpGet("http://localhost:" + myRestfulServerExtension.getPort() + "/$graphql?query=" + UrlUtil.escapeUrlParam("{name{family,given}}"));
 		CloseableHttpResponse status = ourClient.execute(httpGet);
 		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
@@ -215,20 +214,33 @@ public class GraphQLR4RawTest {
 
 	}
 
+	@AfterAll
+	public static void afterClassClearContext() throws Exception {
+		ourClient.close();
+		TestUtil.randomizeLocaleAndTimezone();
+	}
+
+	@BeforeAll
+	public static void beforeClass() throws Exception {
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+	}
+
 	public static class MyGraphQLProvider {
 
-		@GraphQL(type=RequestTypeEnum.GET)
+		@GraphQL(type = RequestTypeEnum.GET)
 		public String processGet(@IdParam IdType theId, @GraphQLQueryUrl String theQuery) {
-			ourMethodCount++;
 			ourLastId = theId;
 			ourLastQuery = theQuery;
 			return ourNextRetVal;
 		}
 
-		@GraphQL(type=RequestTypeEnum.POST)
+		@GraphQL(type = RequestTypeEnum.POST)
-		public String processPost(@IdParam IdType theId, @GraphQLQueryBody String theQuery) {
+		public String processPost(RequestDetails theRequestDetails, @IdParam IdType theId, @GraphQLQueryBody String theQuery) {
-			ourMethodCount++;
 			ourLastId = theId;
+			ourLastResourceType = theRequestDetails.getResourceName();
 			ourLastQuery = theQuery;
 			return ourNextRetVal;
 		}
@@ -246,13 +258,13 @@ public class GraphQLR4RawTest {
 		@Search()
 		public List search(
 			@OptionalParam(name = Patient.SP_IDENTIFIER) TokenAndListParam theIdentifiers) {
-			ArrayList<Patient> retVal = new ArrayList<Patient>();
+			ArrayList<Patient> retVal = new ArrayList<>();
 
 			for (int i = 0; i < 200; i++) {
 				Patient patient = new Patient();
 				patient.addName(new HumanName().setFamily("FAMILY"));
 				patient.getIdElement().setValue("Patient/" + i);
-				retVal.add((Patient) patient);
+				retVal.add(patient);
 			}
 			return retVal;
 		}

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

@@ -3,8 +3,10 @@ package ca.uhn.fhir.util;
 import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
+import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Period;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
@@ -88,6 +90,53 @@ public class GraphQLEngineTest {
 
 	}
 
+
+	@Test
+	public void testChoiceType_SelectDifferentType() throws EGraphEngine, EGraphQLException, IOException {
+		Observation obs = new Observation();
+		obs.setId("http://foo.com/Patient/PATA");
+		obs.setEffective(new Period().setStartElement(new DateTimeType("2022-01-01T00:00:00Z")).setEndElement(new DateTimeType("2022-01-01T05:00:00Z")));
+
+		GraphQLEngine engine = new GraphQLEngine(ourWorkerCtx);
+		engine.setFocus(obs);
+		engine.setGraphQL(Parser.parse("{id, effectiveDateTime}"));
+		engine.execute();
+
+		GraphQLResponse output = engine.getOutput();
+		output.setWriteWrapper(false);
+		StringBuilder outputBuilder = new StringBuilder();
+		output.write(outputBuilder, 0, "\n");
+
+		String expected = "{\n" +
+			"  \"id\":\"http://foo.com/Patient/PATA\"\n" +
+			"}";
+		assertEquals(TestUtil.stripReturns(expected), TestUtil.stripReturns(outputBuilder.toString()));
+	}
+
+	@Test
+	public void testChoiceType_SelectSameType() throws EGraphEngine, EGraphQLException, IOException {
+		Observation obs = new Observation();
+		obs.setId("http://foo.com/Patient/PATA");
+		obs.setEffective(new DateTimeType("2022-01-01T12:12:12Z"));
+
+		GraphQLEngine engine = new GraphQLEngine(ourWorkerCtx);
+		engine.setFocus(obs);
+		engine.setGraphQL(Parser.parse("{id, effectiveDateTime}"));
+		engine.execute();
+
+		GraphQLResponse output = engine.getOutput();
+		output.setWriteWrapper(false);
+		StringBuilder outputBuilder = new StringBuilder();
+		output.write(outputBuilder, 0, "\n");
+
+		String expected = "{\n" +
+			"  \"id\":\"http://foo.com/Patient/PATA\",\n" +
+			"  \"effectiveDateTime\":\"2022-01-01T12:12:12Z\"\n" +
+			"}";
+		assertEquals(TestUtil.stripReturns(expected), TestUtil.stripReturns(outputBuilder.toString()));
+	}
+
+
 	@Test
 	public void testReferences() throws EGraphQLException, EGraphEngine, IOException, FHIRException {
 
@@ -128,7 +177,7 @@ public class GraphQLEngineTest {
 
 	@BeforeAll
 	public static void beforeClass() {
-		ourCtx = FhirContext.forR4();
+		ourCtx = FhirContext.forR4Cached();
 		ourWorkerCtx = new HapiWorkerContext(ourCtx, ourCtx.getValidationSupport());
 	}
 

hapi-fhir-structures-r5/src/test/java/org/hl7/fhir/r5/utils/GraphQLEngineTest.java

@@ -0,0 +1,184 @@
+package org.hl7.fhir.r5.utils;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
+import org.hl7.fhir.r5.model.DateTimeType;
+import org.hl7.fhir.r5.model.Observation;
+import org.hl7.fhir.r5.model.Patient;
+import org.hl7.fhir.r5.model.Period;
+import org.hl7.fhir.r5.model.Quantity;
+import org.hl7.fhir.r5.model.Reference;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.utilities.graphql.EGraphEngine;
+import org.hl7.fhir.utilities.graphql.EGraphQLException;
+import org.hl7.fhir.utilities.graphql.GraphQLResponse;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
+import org.hl7.fhir.utilities.graphql.Parser;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+
+import java.io.IOException;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+public class GraphQLEngineTest {
+	private static HapiWorkerContext ourWorkerCtx;
+	private static FhirContext ourCtx;
+	private org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GraphQLEngineTest.class);
+
+	private Observation createObservation() {
+		Observation obs = new Observation();
+		obs.setId("http://foo.com/Patient/PATA");
+		obs.setValue(new Quantity().setValue(123).setUnit("cm"));
+		obs.setSubject(new Reference("Patient/123"));
+		return obs;
+	}
+
+	private IGraphQLStorageServices createStorageServices() throws FHIRException {
+		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) {
+				Object appInfo = invocation.getArguments()[0];
+				Resource context = (Resource) invocation.getArguments()[1];
+				Reference reference = (Reference) invocation.getArguments()[2];
+				ourLog.info("AppInfo: {} / Context: {} / Reference: {}", appInfo, context.getId(), reference.getReference());
+
+				if (reference.getReference().equalsIgnoreCase("Patient/123")) {
+					Patient p = new Patient();
+					p.getBirthDateElement().setValueAsString("2011-02-22");
+					return new IGraphQLStorageServices.ReferenceResolution(context, p);
+				}
+
+				ourLog.info("Not found!");
+				return null;
+			}
+		});
+
+		return retVal;
+	}
+
+	@Test
+	public void testGraphSimple() throws EGraphQLException, EGraphEngine, IOException, FHIRException {
+
+		Observation obs = createObservation();
+
+		GraphQLEngine engine = new GraphQLEngine(ourWorkerCtx);
+		engine.setFocus(obs);
+		engine.setGraphQL(Parser.parse("{valueQuantity{value,unit}}"));
+		engine.execute();
+
+		GraphQLResponse output = engine.getOutput();
+		output.setWriteWrapper(false);
+		StringBuilder outputBuilder = new StringBuilder();
+		output.write(outputBuilder, 0, "\n");
+
+		String expected = "{\n" +
+			"  \"valueQuantity\":{\n" +
+			"    \"value\":123,\n" +
+			"    \"unit\":\"cm\"\n" +
+			"  }\n" +
+			"}";
+		assertEquals(TestUtil.stripReturns(expected), TestUtil.stripReturns(outputBuilder.toString()));
+
+	}
+
+
+	@Test
+	public void testChoiceType_SelectDifferentType() throws EGraphEngine, EGraphQLException, IOException {
+		Observation obs = new Observation();
+		obs.setId("http://foo.com/Patient/PATA");
+		obs.setEffective(new Period().setStartElement(new DateTimeType("2022-01-01T00:00:00Z")).setEndElement(new DateTimeType("2022-01-01T05:00:00Z")));
+
+		GraphQLEngine engine = new GraphQLEngine(ourWorkerCtx);
+		engine.setFocus(obs);
+		engine.setGraphQL(Parser.parse("{id, effectiveDateTime}"));
+		engine.execute();
+
+		GraphQLResponse output = engine.getOutput();
+		output.setWriteWrapper(false);
+		StringBuilder outputBuilder = new StringBuilder();
+		output.write(outputBuilder, 0, "\n");
+
+		String expected = "{\n" +
+			"  \"id\":\"http://foo.com/Patient/PATA\"\n" +
+			"}";
+		assertEquals(TestUtil.stripReturns(expected), TestUtil.stripReturns(outputBuilder.toString()));
+	}
+
+	@Test
+	public void testChoiceType_SelectSameType() throws EGraphEngine, EGraphQLException, IOException {
+		Observation obs = new Observation();
+		obs.setId("http://foo.com/Patient/PATA");
+		obs.setEffective(new DateTimeType("2022-01-01T12:12:12Z"));
+
+		GraphQLEngine engine = new GraphQLEngine(ourWorkerCtx);
+		engine.setFocus(obs);
+		engine.setGraphQL(Parser.parse("{id, effectiveDateTime}"));
+		engine.execute();
+
+		GraphQLResponse output = engine.getOutput();
+		output.setWriteWrapper(false);
+		StringBuilder outputBuilder = new StringBuilder();
+		output.write(outputBuilder, 0, "\n");
+
+		String expected = "{\n" +
+			"  \"id\":\"http://foo.com/Patient/PATA\",\n" +
+			"  \"effectiveDateTime\":\"2022-01-01T12:12:12Z\"\n" +
+			"}";
+		assertEquals(TestUtil.stripReturns(expected), TestUtil.stripReturns(outputBuilder.toString()));
+	}
+
+
+	@Test
+	public void testReferences() throws EGraphQLException, EGraphEngine, IOException, FHIRException {
+
+		String graph = " { \n" +
+			"  id\n" +
+			"  subject { \n" +
+			"   reference\n" +
+			"    resource(type : Patient) { birthDate }\n" +
+			"    resource(type : Practioner) { practitionerRole {  speciality } }\n" +
+			"  }  \n" +
+			"  code {coding {system code} }\n" +
+			" }\n" +
+			" ";
+
+		GraphQLEngine engine = new GraphQLEngine(ourWorkerCtx);
+		engine.setFocus(createObservation());
+		engine.setGraphQL(Parser.parse(graph));
+		engine.setServices(createStorageServices());
+		engine.execute();
+
+		GraphQLResponse output = engine.getOutput();
+		output.setWriteWrapper(false);
+		StringBuilder outputBuilder = new StringBuilder();
+		output.write(outputBuilder, 0, "\n");
+
+		String expected = "{\n" +
+			"  \"id\":\"http://foo.com/Patient/PATA\",\n" +
+			"  \"subject\":{\n" +
+			"    \"reference\":\"Patient/123\",\n" +
+			"    \"resource\":{\n" +
+			"      \"birthDate\":\"2011-02-22\"\n" +
+			"    }\n" +
+			"  }\n" +
+			"}";
+		assertEquals(TestUtil.stripReturns(expected), TestUtil.stripReturns(outputBuilder.toString()));
+
+	}
+
+	@BeforeAll
+	public static void beforeClass() {
+		ourCtx = FhirContext.forR5Cached();
+		ourWorkerCtx = new HapiWorkerContext(ourCtx, ourCtx.getValidationSupport());
+	}
+
+}

pom.xml

@@ -45,15 +45,6 @@
 	</scm>
 
 	<repositories>
-		<!--
-		<repository>
-			<id>jitpack.io</id>
-			<url>https://jitpack.io</url>
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-		</repository>
-		-->
 		<repository>
 			<id>oss-snapshot</id>
 			<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
@@ -765,7 +756,7 @@
 
     <properties>
 
-        <fhir_core_version>5.6.27</fhir_core_version>
+        <fhir_core_version>5.6.35</fhir_core_version>
         <ucum_version>1.0.3</ucum_version>
 
         <surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
@@ -924,6 +915,11 @@
 				<artifactId>caffeine</artifactId>
 				<version>${caffeine_version}</version>
 			</dependency>
+			<dependency>
+				<groupId>com.graphql-java</groupId>
+				<artifactId>graphql-java</artifactId>
+				<version>17.3</version>
+			</dependency>
 			<!-- mail start -->
 			<dependency>
 				<groupId>org.simplejavamail</groupId>