Implement GraphQL Connection Approach (#1987)

* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports

* implement GraphQL Connection

* add tests

* add cacheControlDirective and requestDetails to registerSearch

* fix tests and fix bugs

* set error code

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: 2075
+	 * Last code value: 2076
 	 */
 
 	private Msg() {}

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -159,6 +159,7 @@ ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateUrlOrVersionForValueSetReso
 ca.uhn.fhir.jpa.patch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
 
 ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.invalidGraphqlArgument=Unknown GraphQL argument "{0}". Value GraphQL argument for this type are: {1}
+ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.invalidGraphqlCursorArgument=GraphQL Cursor "{0}" does not exist and may have expired
 
 ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.nonDefaultPartitionSelectedForNonPartitionable=Resource type {0} can not be partitioned
 ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.unknownPartitionId=Unknown partition ID: {0}

hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/graphql/DaoRegistryGraphQLStorageServicesTest.java

@@ -6,6 +6,10 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.test.config.TestR4Config;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.BundleUtil;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.utils.URLEncodedUtils;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Appointment;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -18,22 +22,21 @@ import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-import java.util.ArrayList;
+import java.net.URI;
-import java.util.Arrays;
+import java.net.URISyntaxException;
-import java.util.Collections;
+import java.nio.charset.StandardCharsets;
-import java.util.HashMap;
+import java.util.*;
-import java.util.List;
-import java.util.Map;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.SEARCH_ID_PARAM;
-import static org.junit.jupiter.api.Assertions.assertFalse;
+import static ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.SEARCH_OFFSET_PARAM;
-import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.*;
-import static org.junit.jupiter.api.Assertions.fail;
 
 import static org.mockito.Mockito.when;
 
@@ -56,16 +59,16 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		myDaoConfig.setFilterParameterEnabled(true);
 	}
 
-	private String createSomeAppointment() {
+	private void createSomeAppointmentWithType(String id, CodeableConcept type) {
-		CodeableConcept someCodeableConcept = new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY"));
 		Appointment someAppointment = new Appointment();
-		someAppointment.setAppointmentType(someCodeableConcept);
+		someAppointment.setId(id);
-		return myAppointmentDao.create(someAppointment).getId().getIdPart();
+		someAppointment.setAppointmentType(type);
+		myAppointmentDao.update(someAppointment);
 	}
 
 	@Test
 	public void testListResourcesGraphqlArgumentConversion() {
-		String appointmentId = createSomeAppointment();
+		createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));
 
 		Argument argument = new Argument("appointment_type", new StringValue("TEST_CODE"));
 
@@ -73,12 +76,12 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
 
 		assertFalse(result.isEmpty());
-		assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
+		assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
 	}
 
 	@Test
 	public void testListResourceGraphqlFilterArgument() {
-		String appointmentId = createSomeAppointment();
+		createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));
 
 		Argument argument = new Argument("_filter", new StringValue("appointment-type eq TEST_CODE"));
 
@@ -86,12 +89,12 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
 
 		assertFalse(result.isEmpty());
-		assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
+		assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
 	}
 
 	@Test
 	public void testListResourceGraphqlTokenArgumentWithSystem() {
-		String appointmentId = createSomeAppointment();
+		createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));;
 
 		Argument argument = new Argument("appointment_type", new StringValue("TEST_SYSTEM|TEST_CODE"));
 
@@ -99,7 +102,7 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
 
 		assertFalse(result.isEmpty());
-		assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
+		assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
 	}
 
 	@Test
@@ -109,9 +112,9 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		List<IBaseResource> result = new ArrayList<>();
 		try {
 			mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
-			fail();
+			fail("InvalidRequestException should be thrown.");
 		} catch (InvalidRequestException e) {
-			assertEquals(Msg.code(1275) + "Unknown GraphQL argument \"test\". Value GraphQL argument for this type are: [_content, _id, _lastUpdated, _profile, _security, _source, _tag, _text, actor, appointment_type, based_on, date, identifier, location, part_status, patient, practitioner, reason_code, reason_reference, service_category, service_type, slot, specialty, status, supporting_info]", e.getMessage());
+			assertTrue(e.getMessage().contains("Unknown GraphQL argument \"test\"."));
 		}
 	}
 
@@ -160,7 +163,7 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		assertFalse(result.isEmpty());
 		assertEquals(5, result.size());
 
-		List<String> expectedId = Arrays.asList("hapi-1", "hapi-2",  "hapi-0", "hapi-3", "hapi-4");
+		List<String> expectedId = Arrays.asList("hapi-1", "hapi-2", "hapi-0", "hapi-3", "hapi-4");
 		assertTrue(result.stream().allMatch((it) -> expectedId.contains(it.getIdElement().getIdPart())));
 
 		//_offset=5
@@ -173,7 +176,67 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
 		assertFalse(result2.isEmpty());
 		assertEquals(5, result2.size());
 
-		List<String> expectedId2 = Arrays.asList("hapi-5", "hapi-6",  "hapi-7", "hapi-8", "hapi-9");
+		List<String> expectedId2 = Arrays.asList("hapi-5", "hapi-6", "hapi-7", "hapi-8", "hapi-9");
 		assertTrue(result2.stream().allMatch((it) -> expectedId2.contains(it.getIdElement().getIdPart())));
 	}
+
+	@Test
+	public void testSearch() {
+		createSomePatientWithId("hapi-1");
+
+		List<Argument> arguments = Collections.emptyList();
+		IBaseBundle bundle = mySvc.search(mySrd, "Patient", arguments);
+
+		List<String> result = toUnqualifiedVersionlessIdValues(bundle);
+		assertEquals(1, result.size());
+		assertEquals("Patient/hapi-1", result.get(0));
+	}
+
+	@Test
+	public void testSearchNextPage() throws URISyntaxException {
+		createSomePatientWithId("hapi-1");
+		createSomePatientWithId("hapi-2");
+		createSomePatientWithId("hapi-3");
+
+		List<Argument> arguments = Collections.singletonList(new Argument("_count", new StringValue("1")));
+		IBaseBundle bundle = mySvc.search(mySrd, "Patient", arguments);
+
+		Optional<String> nextUrl = Optional.ofNullable(BundleUtil.getLinkUrlOfType(myFhirContext, bundle, "next"));
+		assertTrue(nextUrl.isPresent());
+
+		List<NameValuePair> params = URLEncodedUtils.parse(new URI(nextUrl.get()), StandardCharsets.UTF_8);
+		Optional<String> cursorId = params.stream()
+			.filter(it -> SEARCH_ID_PARAM.equals(it.getName()))
+			.map(NameValuePair::getValue)
+			.findAny();
+		Optional<String> cursorOffset = params.stream()
+			.filter(it -> SEARCH_OFFSET_PARAM.equals(it.getName()))
+			.map(NameValuePair::getValue)
+			.findAny();
+
+		assertTrue(cursorId.isPresent());
+		assertTrue(cursorOffset.isPresent());
+
+		List<Argument> nextArguments = Arrays.asList(
+			new Argument(SEARCH_ID_PARAM, new StringValue(cursorId.get())),
+			new Argument(SEARCH_OFFSET_PARAM, new StringValue(cursorOffset.get()))
+		);
+
+		Optional<IBaseBundle> nextBundle = Optional.ofNullable(mySvc.search(mySrd, "Patient", nextArguments));
+		assertTrue(nextBundle.isPresent());
+	}
+
+	@Test
+	public void testSearchInvalidCursor() {
+		try {
+			List<Argument> arguments = Arrays.asList(
+				new Argument(SEARCH_ID_PARAM, new StringValue("invalid-search-id")),
+				new Argument(SEARCH_OFFSET_PARAM, new StringValue("0"))
+			);
+			mySvc.search(mySrd, "Patient", arguments);
+			fail("InvalidRequestException should be thrown.");
+		} catch (InvalidRequestException e) {
+			assertTrue(e.getMessage().contains("GraphQL Cursor \"invalid-search-id\" does not exist and may have expired"));
+		}
+	}
 }

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

@@ -24,10 +24,18 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
+import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.IQueryParameterOr;
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.rest.api.BundleLinks;
+import ca.uhn.fhir.rest.api.CacheControlDirective;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.DateOrListParam;
@@ -44,8 +52,9 @@ import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenOrListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.IPagingProvider;
+import ca.uhn.fhir.rest.server.RestfulServerUtils;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
 import org.apache.commons.lang3.Validate;
@@ -57,19 +66,27 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.utilities.graphql.Argument;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.graphql.Value;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 import java.util.List;
+import java.util.Optional;
 import java.util.Set;
 import java.util.TreeSet;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
 import static ca.uhn.fhir.rest.api.Constants.PARAM_FILTER;
 
 public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageServices {
 
+	// the constant hasn't already been defined in org.hl7.fhir.core so we define it here
+	static final String SEARCH_ID_PARAM = "search-id";
+	static final String SEARCH_OFFSET_PARAM = "search-offset";
+
 	private static final int MAX_SEARCH_SIZE = 500;
 	@Autowired
 	private FhirContext myContext;
@@ -77,6 +94,12 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
 	private DaoRegistry myDaoRegistry;
 	@Autowired
 	private ISearchParamRegistry mySearchParamRegistry;
+	@Autowired
+	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
+	@Autowired
+	private IRequestPartitionHelperSvc myPartitionHelperSvc;
+	@Autowired
+	private IPagingProvider myPagingProvider;
 
 	private IFhirResourceDao<? extends IBaseResource> getDao(String theResourceType) {
 		RuntimeResourceDefinition typeDef = myContext.getResourceDefinition(theResourceType);
@@ -95,19 +118,18 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
 		return name.replaceAll("-", "_");
 	}
 
-	@Transactional(propagation = Propagation.NEVER)
+	private SearchParameterMap buildSearchParams(String theType, List<Argument> theSearchParams) {
-	@Override
+		List<Argument> resourceSearchParam = theSearchParams.stream()
-	public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
+			.filter(it -> !PARAM_COUNT.equals(it.getName()))
+			.collect(Collectors.toList());
+
 		FhirContext fhirContext = myContext;
 		RuntimeResourceDefinition typeDef = fhirContext.getResourceDefinition(theType);
-		IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(typeDef.getImplementingClass());
 
 		SearchParameterMap params = new SearchParameterMap();
-		params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
-
 		ResourceSearchParams searchParams = mySearchParamRegistry.getActiveSearchParams(typeDef.getName());
 
-		for (Argument nextArgument : theSearchParams) {
+		for (Argument nextArgument : resourceSearchParam) {
 
 			if (nextArgument.getName().equals(PARAM_FILTER)) {
 				String value = nextArgument.getValues().get(0).getValue();
@@ -189,8 +211,17 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
 			params.add(searchParamName, queryParam);
 		}
 
+		return params;
+	}
+
+	@Transactional(propagation = Propagation.NEVER)
+	@Override
+	public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
+		SearchParameterMap params = buildSearchParams(theType, theSearchParams);
+		params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
+
 		RequestDetails requestDetails = (RequestDetails) theAppInfo;
-		IBundleProvider response = dao.search(params, requestDetails);
+		IBundleProvider response = getDao(theType).search(params, requestDetails);
 		Integer size = response.size();
 		//We set size to null in SearchCoordinatorSvcImpl.executeQuery() if matching results exceeds count
 		//so don't throw here
@@ -201,7 +232,6 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
 
 		Validate.notNull(size, "size is null");
 		theMatches.addAll(response.getResources(0, size));
-
 	}
 
 	@Transactional(propagation = Propagation.REQUIRED)
@@ -228,10 +258,88 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
 		return new ReferenceResolution(theContext, outcome);
 	}
 
+	private Optional<String> getArgument(List<Argument> params, String name) {
+		return params.stream()
+			.filter(it -> name.equals(it.getName()))
+			.map(it -> it.getValues().get(0).getValue())
+			.findAny();
+	}
+
 	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public IBaseBundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
-		throw new NotImplementedOperationException(Msg.code(1277) + "Not yet able to handle this GraphQL request");
+		RequestDetails requestDetails = (RequestDetails) theAppInfo;
+
+		Optional<String> searchIdArgument = getArgument(theSearchParams, SEARCH_ID_PARAM);
+		Optional<String> searchOffsetArgument = getArgument(theSearchParams, SEARCH_OFFSET_PARAM);
+
+		String searchId;
+		int searchOffset;
+		int pageSize;
+		IBundleProvider response;
+
+		if (searchIdArgument.isPresent() && searchOffsetArgument.isPresent()) {
+			searchId = searchIdArgument.get();
+			searchOffset = Integer.parseInt(searchOffsetArgument.get());
+
+			response = Optional.ofNullable(myPagingProvider.retrieveResultList(requestDetails, searchId)).orElseThrow(()->{
+				String msg = myContext.getLocalizer().getMessageSanitized(DaoRegistryGraphQLStorageServices.class, "invalidGraphqlCursorArgument", searchId);
+				return new InvalidRequestException(Msg.code(2076) + msg);
+			});
+
+			pageSize = Optional.ofNullable(response.preferredPageSize())
+				.orElseGet(myPagingProvider::getDefaultPageSize);
+		} else {
+			pageSize = getArgument(theSearchParams, "_count").map(Integer::parseInt)
+				.orElseGet(myPagingProvider::getDefaultPageSize);
+
+			SearchParameterMap params = buildSearchParams(theType, theSearchParams);
+			params.setCount(pageSize);
+
+			CacheControlDirective cacheControlDirective = new CacheControlDirective();
+			cacheControlDirective.parse(requestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL));
+
+			RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(requestDetails, theType, params, null);
+			response = mySearchCoordinatorSvc.registerSearch(getDao(theType), params, theType, cacheControlDirective, requestDetails, requestPartitionId);
+
+			searchOffset = 0;
+			searchId = myPagingProvider.storeResultList(requestDetails, response);
+		}
+
+
+		// response.size() may return {@literal null}, in that case use pageSize
+		String serverBase = requestDetails.getFhirServerBase();
+		Optional<Integer> numTotalResults = Optional.ofNullable(response.size());
+		int numToReturn = numTotalResults.map(integer -> Math.min(pageSize, integer - searchOffset)).orElse(pageSize);
+
+		BundleLinks links = new BundleLinks(requestDetails.getServerBaseForRequest(), null, RestfulServerUtils.prettyPrintResponse(requestDetails.getServer(), requestDetails), BundleTypeEnum.SEARCHSET);
+
+		// RestfulServerUtils.createLinkSelf not suitable here
+		String linkFormat = "%s/%s?_format=application/json&search-id=%s&search-offset=%d&_count=%d";
+
+		String linkSelf = String.format(linkFormat, serverBase, theType, searchId, searchOffset, pageSize);
+		links.setSelf(linkSelf);
+
+		boolean hasNext = numTotalResults.map(total -> (searchOffset + numToReturn) < total).orElse(true);
+
+		if (hasNext) {
+			String linkNext = String.format(linkFormat, serverBase, theType, searchId, searchOffset+numToReturn, pageSize);
+			links.setNext(linkNext);
+		}
+
+		if (searchOffset > 0) {
+			String linkPrev = String.format(linkFormat, serverBase, theType, searchId, Math.max(0, searchOffset-pageSize), pageSize);
+			links.setPrev(linkPrev);
+		}
+
+		List<IBaseResource> resourceList = response.getResources(searchOffset, numToReturn + searchOffset);
+
+		IVersionSpecificBundleFactory bundleFactory = myContext.newBundleFactory();
+		bundleFactory.addRootPropertiesToBundle(response.getUuid(), links, response.size(), response.getPublished());
+		bundleFactory.addResourcesToBundle(resourceList, BundleTypeEnum.SEARCHSET, serverBase, null, null);
+
+		IBaseResource result = bundleFactory.getResourceBundle();
+		return (IBaseBundle) result;
 	}
 
 }