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
This commit is contained in:
Ibrohim Kholilul Islam
GitHub
parent
5dfdc91682
commit
d20c6a7d25
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@ -25,7 +25,7 @@ public final class Msg {
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/**
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* IMPORTANT: Please update the following comment after you add a new code
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* Last code value: 2075
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* Last code value: 2076
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*/
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private Msg() {}
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@ -159,6 +159,7 @@ ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateUrlOrVersionForValueSetReso
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ca.uhn.fhir.jpa.patch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
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ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.invalidGraphqlArgument=Unknown GraphQL argument "{0}". Value GraphQL argument for this type are: {1}
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ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.invalidGraphqlCursorArgument=GraphQL Cursor "{0}" does not exist and may have expired
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ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.nonDefaultPartitionSelectedForNonPartitionable=Resource type {0} can not be partitioned
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ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.unknownPartitionId=Unknown partition ID: {0}
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@ -6,6 +6,10 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.test.config.TestR4Config;
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import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.util.BundleUtil;
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import org.apache.http.NameValuePair;
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import org.apache.http.client.utils.URLEncodedUtils;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.Appointment;
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import org.hl7.fhir.r4.model.CodeableConcept;
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@ -18,22 +22,21 @@ import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.annotation.DirtiesContext;
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import org.springframework.test.context.ContextConfiguration;
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import org.springframework.test.context.junit.jupiter.SpringExtension;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.nio.charset.StandardCharsets;
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import java.util.*;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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import static ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.SEARCH_ID_PARAM;
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import static ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.SEARCH_OFFSET_PARAM;
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import static org.junit.jupiter.api.Assertions.*;
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import static org.mockito.Mockito.when;
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@ -56,16 +59,16 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
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myDaoConfig.setFilterParameterEnabled(true);
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}
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private String createSomeAppointment() {
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CodeableConcept someCodeableConcept = new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY"));
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private void createSomeAppointmentWithType(String id, CodeableConcept type) {
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Appointment someAppointment = new Appointment();
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someAppointment.setAppointmentType(someCodeableConcept);
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return myAppointmentDao.create(someAppointment).getId().getIdPart();
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someAppointment.setId(id);
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someAppointment.setAppointmentType(type);
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myAppointmentDao.update(someAppointment);
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}
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@Test
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public void testListResourcesGraphqlArgumentConversion() {
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String appointmentId = createSomeAppointment();
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createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));
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Argument argument = new Argument("appointment_type", new StringValue("TEST_CODE"));
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@ -73,12 +76,12 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
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mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
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assertFalse(result.isEmpty());
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assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
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assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
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}
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@Test
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public void testListResourceGraphqlFilterArgument() {
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String appointmentId = createSomeAppointment();
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createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));
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Argument argument = new Argument("_filter", new StringValue("appointment-type eq TEST_CODE"));
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@ -86,12 +89,12 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
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mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
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assertFalse(result.isEmpty());
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assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
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assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
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}
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@Test
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public void testListResourceGraphqlTokenArgumentWithSystem() {
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String appointmentId = createSomeAppointment();
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createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));;
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Argument argument = new Argument("appointment_type", new StringValue("TEST_SYSTEM|TEST_CODE"));
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@ -99,7 +102,7 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
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mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
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assertFalse(result.isEmpty());
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assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
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assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
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}
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@Test
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@ -109,9 +112,9 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
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List<IBaseResource> result = new ArrayList<>();
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try {
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mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
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fail();
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fail("InvalidRequestException should be thrown.");
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} catch (InvalidRequestException e) {
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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());
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assertTrue(e.getMessage().contains("Unknown GraphQL argument \"test\"."));
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}
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}
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@ -176,4 +179,64 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
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List<String> expectedId2 = Arrays.asList("hapi-5", "hapi-6", "hapi-7", "hapi-8", "hapi-9");
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assertTrue(result2.stream().allMatch((it) -> expectedId2.contains(it.getIdElement().getIdPart())));
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}
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@Test
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public void testSearch() {
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createSomePatientWithId("hapi-1");
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List<Argument> arguments = Collections.emptyList();
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IBaseBundle bundle = mySvc.search(mySrd, "Patient", arguments);
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List<String> result = toUnqualifiedVersionlessIdValues(bundle);
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assertEquals(1, result.size());
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assertEquals("Patient/hapi-1", result.get(0));
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}
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@Test
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public void testSearchNextPage() throws URISyntaxException {
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createSomePatientWithId("hapi-1");
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createSomePatientWithId("hapi-2");
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createSomePatientWithId("hapi-3");
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List<Argument> arguments = Collections.singletonList(new Argument("_count", new StringValue("1")));
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IBaseBundle bundle = mySvc.search(mySrd, "Patient", arguments);
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Optional<String> nextUrl = Optional.ofNullable(BundleUtil.getLinkUrlOfType(myFhirContext, bundle, "next"));
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assertTrue(nextUrl.isPresent());
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List<NameValuePair> params = URLEncodedUtils.parse(new URI(nextUrl.get()), StandardCharsets.UTF_8);
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Optional<String> cursorId = params.stream()
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.filter(it -> SEARCH_ID_PARAM.equals(it.getName()))
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.map(NameValuePair::getValue)
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.findAny();
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Optional<String> cursorOffset = params.stream()
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.filter(it -> SEARCH_OFFSET_PARAM.equals(it.getName()))
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.map(NameValuePair::getValue)
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.findAny();
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assertTrue(cursorId.isPresent());
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assertTrue(cursorOffset.isPresent());
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List<Argument> nextArguments = Arrays.asList(
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new Argument(SEARCH_ID_PARAM, new StringValue(cursorId.get())),
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new Argument(SEARCH_OFFSET_PARAM, new StringValue(cursorOffset.get()))
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);
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Optional<IBaseBundle> nextBundle = Optional.ofNullable(mySvc.search(mySrd, "Patient", nextArguments));
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assertTrue(nextBundle.isPresent());
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}
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@Test
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public void testSearchInvalidCursor() {
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try {
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List<Argument> arguments = Arrays.asList(
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new Argument(SEARCH_ID_PARAM, new StringValue("invalid-search-id")),
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new Argument(SEARCH_OFFSET_PARAM, new StringValue("0"))
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);
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mySvc.search(mySrd, "Patient", arguments);
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fail("InvalidRequestException should be thrown.");
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} catch (InvalidRequestException e) {
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assertTrue(e.getMessage().contains("GraphQL Cursor \"invalid-search-id\" does not exist and may have expired"));
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}
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}
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}
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@ -24,10 +24,18 @@ import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
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import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.model.api.IQueryParameterOr;
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import ca.uhn.fhir.model.valueset.BundleTypeEnum;
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import ca.uhn.fhir.rest.api.BundleLinks;
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import ca.uhn.fhir.rest.api.CacheControlDirective;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.param.DateOrListParam;
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@ -44,8 +52,9 @@ import ca.uhn.fhir.rest.param.StringOrListParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenOrListParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.server.IPagingProvider;
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import ca.uhn.fhir.rest.server.RestfulServerUtils;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
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import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
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import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
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import org.apache.commons.lang3.Validate;
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@ -57,19 +66,27 @@ import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.utilities.graphql.Argument;
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import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
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import org.hl7.fhir.utilities.graphql.Value;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.annotation.Propagation;
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import org.springframework.transaction.annotation.Transactional;
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import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import java.util.TreeSet;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_FILTER;
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public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageServices {
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// the constant hasn't already been defined in org.hl7.fhir.core so we define it here
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static final String SEARCH_ID_PARAM = "search-id";
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static final String SEARCH_OFFSET_PARAM = "search-offset";
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private static final int MAX_SEARCH_SIZE = 500;
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@Autowired
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private FhirContext myContext;
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@ -77,6 +94,12 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
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private DaoRegistry myDaoRegistry;
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@Autowired
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private ISearchParamRegistry mySearchParamRegistry;
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@Autowired
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protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
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@Autowired
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private IRequestPartitionHelperSvc myPartitionHelperSvc;
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@Autowired
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private IPagingProvider myPagingProvider;
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private IFhirResourceDao<? extends IBaseResource> getDao(String theResourceType) {
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RuntimeResourceDefinition typeDef = myContext.getResourceDefinition(theResourceType);
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@ -95,19 +118,18 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
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return name.replaceAll("-", "_");
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}
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@Transactional(propagation = Propagation.NEVER)
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@Override
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public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
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private SearchParameterMap buildSearchParams(String theType, List<Argument> theSearchParams) {
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List<Argument> resourceSearchParam = theSearchParams.stream()
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.filter(it -> !PARAM_COUNT.equals(it.getName()))
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.collect(Collectors.toList());
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FhirContext fhirContext = myContext;
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RuntimeResourceDefinition typeDef = fhirContext.getResourceDefinition(theType);
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IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(typeDef.getImplementingClass());
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
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ResourceSearchParams searchParams = mySearchParamRegistry.getActiveSearchParams(typeDef.getName());
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for (Argument nextArgument : theSearchParams) {
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for (Argument nextArgument : resourceSearchParam) {
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if (nextArgument.getName().equals(PARAM_FILTER)) {
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String value = nextArgument.getValues().get(0).getValue();
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@ -189,8 +211,17 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
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params.add(searchParamName, queryParam);
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}
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return params;
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}
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@Transactional(propagation = Propagation.NEVER)
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@Override
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public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
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SearchParameterMap params = buildSearchParams(theType, theSearchParams);
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params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
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RequestDetails requestDetails = (RequestDetails) theAppInfo;
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IBundleProvider response = dao.search(params, requestDetails);
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IBundleProvider response = getDao(theType).search(params, requestDetails);
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Integer size = response.size();
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//We set size to null in SearchCoordinatorSvcImpl.executeQuery() if matching results exceeds count
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//so don't throw here
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@ -201,7 +232,6 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
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Validate.notNull(size, "size is null");
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theMatches.addAll(response.getResources(0, size));
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}
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@Transactional(propagation = Propagation.REQUIRED)
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@ -228,10 +258,88 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
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return new ReferenceResolution(theContext, outcome);
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}
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private Optional<String> getArgument(List<Argument> params, String name) {
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return params.stream()
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.filter(it -> name.equals(it.getName()))
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.map(it -> it.getValues().get(0).getValue())
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.findAny();
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}
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@Transactional(propagation = Propagation.NEVER)
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@Override
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public IBaseBundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
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throw new NotImplementedOperationException(Msg.code(1277) + "Not yet able to handle this GraphQL request");
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RequestDetails requestDetails = (RequestDetails) theAppInfo;
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Optional<String> searchIdArgument = getArgument(theSearchParams, SEARCH_ID_PARAM);
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Optional<String> searchOffsetArgument = getArgument(theSearchParams, SEARCH_OFFSET_PARAM);
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String searchId;
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int searchOffset;
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int pageSize;
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IBundleProvider response;
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if (searchIdArgument.isPresent() && searchOffsetArgument.isPresent()) {
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searchId = searchIdArgument.get();
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searchOffset = Integer.parseInt(searchOffsetArgument.get());
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response = Optional.ofNullable(myPagingProvider.retrieveResultList(requestDetails, searchId)).orElseThrow(()->{
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String msg = myContext.getLocalizer().getMessageSanitized(DaoRegistryGraphQLStorageServices.class, "invalidGraphqlCursorArgument", searchId);
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return new InvalidRequestException(Msg.code(2076) + msg);
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});
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pageSize = Optional.ofNullable(response.preferredPageSize())
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.orElseGet(myPagingProvider::getDefaultPageSize);
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} else {
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pageSize = getArgument(theSearchParams, "_count").map(Integer::parseInt)
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.orElseGet(myPagingProvider::getDefaultPageSize);
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SearchParameterMap params = buildSearchParams(theType, theSearchParams);
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params.setCount(pageSize);
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CacheControlDirective cacheControlDirective = new CacheControlDirective();
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cacheControlDirective.parse(requestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL));
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|
||||
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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue