Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook

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

@@ -257,6 +257,29 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testTagsInContainedResourcesPreserved() {
+		Patient p = new Patient();
+		p.setActive(true);
+
+		Organization o = new Organization();
+		o.getMeta().addTag("http://foo", "bar", "FOOBAR");
+		p.getManagingOrganization().setResource(o);
+
+		ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+
+		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		p = myPatientDao.read(id);
+
+		ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p));
+
+		Organization org = (Organization) p.getManagingOrganization().getResource();
+		assertEquals("#1", org.getId());
+		assertEquals(1, org.getMeta().getTag().size());
+
+	}
+
 
 	@AfterClass
 	public static void afterClassClearContext() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -161,7 +161,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		sp.setCode("myDoctor");
 		sp.setType(org.hl7.fhir.r4.model.Enumerations.SearchParamType.REFERENCE);
 		sp.setTitle("My Doctor");
-		sp.setExpression("Patient.extension('http://fmcna.com/myDoctor')");
+		sp.setExpression("Patient.extension('http://fmcna.com/myDoctor').value.as(Reference)");
 		sp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
 		sp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
 		mySearchParameterDao.create(sp);
@@ -184,6 +184,41 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		assertThat(ids, contains(pid.getValue()));
 	}
 
+
+	@Test
+	public void testIndexIntoBundle() {
+		SearchParameter sp = new SearchParameter();
+		sp.addBase("Bundle");
+		sp.setCode("messageid");
+		sp.setType(Enumerations.SearchParamType.TOKEN);
+		sp.setTitle("Message ID");
+		sp.setExpression("Bundle.entry.resource.as(MessageHeader).id");
+		sp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
+		sp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
+		mySearchParameterDao.create(sp);
+
+		mySearchParamRegistry.forceRefresh();
+
+		MessageHeader messageHeader = new MessageHeader();
+		messageHeader.setId("123");
+		Bundle bundle = new Bundle();
+		bundle.setType(Bundle.BundleType.MESSAGE);
+		bundle.addEntry()
+			.setResource(messageHeader);
+
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+		myBundleDao.create(bundle);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add("messageid", new TokenParam("123"));
+		IBundleProvider outcome = myBundleDao.search(params);
+		List<String> ids = toUnqualifiedVersionlessIdValues(outcome);
+		ourLog.info("IDS: " + ids);
+		assertThat(ids, not(empty()));
+	}
+
+
 	@Test
 	public void testExtensionWithNoValueIndexesWithoutFailure() {
 		SearchParameter eyeColourSp = new SearchParameter();
@@ -1075,6 +1110,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		sp.setExpression("Observation.specimen.resolve().receivedTime");
 		sp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
 		sp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
 		mySearchParameterDao.create(sp);
 
 		mySearchParamRegistry.forceRefresh();
@@ -1087,6 +1123,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		o.getContained().add(specimen);
 		o.setStatus(Observation.ObservationStatus.FINAL);
 		o.setSpecimen(new Reference("#FOO"));
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(o));
 		myObservationDao.update(o);
 
 		specimen = new Specimen();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import ca.uhn.fhir.jpa.config.TestR4Config;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -36,6 +35,7 @@ import java.util.concurrent.Future;
 import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.leftPad;
+import static org.awaitility.Awaitility.await;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 
@@ -194,13 +194,17 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
 		params.setSummaryMode(SummaryEnum.DATA);
 		IBundleProvider results = myPatientDao.search(params);
-		String uuid = results.getUuid();
+		final String uuid = results.getUuid();
 		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(200, results.size().intValue());
 		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
-		assertEquals(200, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
+
+		await().until(() -> myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size() != null);
+		results = myDatabaseBackedPagingProvider.retrieveResultList(null, uuid);
+		Integer resultsSize = results.size();
+		assertEquals(200, resultsSize.intValue());
 
 		// Try the same query again. This time the same thing should come back, but
 		// from the cache...
@@ -210,13 +214,14 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		params.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
 		params.setSummaryMode(SummaryEnum.DATA);
 		results = myPatientDao.search(params);
-		uuid = results.getUuid();
+		String uuid2 = results.getUuid();
-		ourLog.info("** Search returned UUID: {}", uuid);
+		assertEquals(uuid, uuid2);
+		ourLog.info("** Search returned UUID: {}", uuid2);
 		assertEquals(200, results.size().intValue());
 		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
-		assertEquals(200, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
+		assertEquals(200, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid2).size().intValue());
 
 	}
 
@@ -250,6 +255,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
+		await().until(() -> myDatabaseBackedPagingProvider.retrieveResultList(null, uuid2).size() != null);
 		IBundleProvider results2 = myDatabaseBackedPagingProvider.retrieveResultList(null, uuid2);
 		Integer results2Size = results2.size();
 		assertEquals(200, results2Size.intValue());