From e8c080bb12fae44b11c10a9c7338ff187731154a Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 13:45:09 -0500
Subject: [PATCH 01/13] Add initial FIXMEs.

---
 .../ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java     | 2 ++
 .../dao/index/SearchParamWithInlineReferencesExtractor.java    | 1 +
 .../main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java    | 1 +
 .../src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java      | 3 +++
 4 files changed, 7 insertions(+)

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
index a65383748ac..f78746bbe6e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
@@ -110,6 +110,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 		return resolvedResource;
 	}
 
+	// FIXME: DM 2021-03-04 - This is where placeholder reference targets are handled.
 	/**
 	 * @param theIdToAssignToPlaceholder If specified, the placeholder resource created will be given a specific ID
 	 */
@@ -123,6 +124,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 			@SuppressWarnings("unchecked")
 			T newResource = (T) missingResourceDef.newInstance();
 
+			// FIXME: DM 2021-03-04 - This is where the placeholder extension is added; should be in resource body instead of meta?
 			IBaseMetaType meta = newResource.getMeta();
 			if (meta instanceof IBaseHasExtensions) {
 				IBaseExtension<?, ?> extension = ((IBaseHasExtensions) meta).addExtension();
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
index 0a059bbc1ab..bdbf6ec991d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
@@ -214,6 +214,7 @@ public class SearchParamWithInlineReferencesExtractor {
 	}
 
 
+	// FIXME: DM 2021-03-04 - This is where inline match URLs are handled.
 	/**
 	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
 	 * matching resource.
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
index 0782e7db872..a5c579e096c 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
@@ -2123,6 +2123,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	private boolean isPlaceholder(MetadataResource theResource) {
+		// FIXME: DM 2021-03-04 - We should probably check if this extension exists and the value is true.
 		return theResource.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER) != null;
 	}
 
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
index eeaa4eac020..1f864c9471e 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
@@ -357,6 +357,9 @@ public class NpmR4Test extends BaseJpaR4Test {
 		}
 	}
 
+	// FIXME: DM 2021-03-04 - This test is meant to validate that placeholder ValueSets are not created.
+	// FIXME: DM 2021-03-04 - This test or a new test should probably validate that placeholder ConceptMaps are also not created.
+	// FIXME: DM 2021-03-04 - This test does not validate that placeholder resources are created with a EXT_RESOURCE_META_PLACEHOLDER extension.
 	// Reproduces https://github.com/hapifhir/hapi-fhir/issues/2332
 	@Test
 	public void testInstallR4Package_AutoCreatePlaceholder() throws Exception {

From 5a952ad9809a8b5d1335781e99361d08d3d7e6c1 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 14:16:14 -0500
Subject: [PATCH 02/13] Add more FIXMEs as my understanding grows.

---
 .../jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index 2278a76de7e..3b296bb9e68 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -7,7 +7,6 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import ca.uhn.fhir.util.TestUtil;
 import com.google.common.collect.Sets;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.AuditEvent;
@@ -18,16 +17,15 @@ import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 
 import java.util.List;
 
 import static org.hamcrest.CoreMatchers.startsWith;
+import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.hamcrest.MatcherAssert.assertThat;
 import static org.junit.jupiter.api.Assertions.fail;
 
 @SuppressWarnings({"ConstantConditions"})
@@ -173,6 +171,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals("Patient/999999999999999", outcome.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless().getValue());
 	}
 
+	// FIXME: DM 2021-03-04 - These ARE the tests you're looking for.
 	@Test
 	public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedByDefault() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
@@ -197,6 +196,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 	public void testCreatePlaceholderWithMatchUrl_IdentifierCopied_NotPreExisting() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		// FIXME: DM - 2021-03-04 - Whaaat?! This is configurable. Awesome. What's the default?
 		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
 
 		Observation obsToCreate = new Observation();

From 9a7bd0e775135f8a0a8470c401d5255de8ba701d Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 16:55:16 -0500
Subject: [PATCH 03/13] Add failing tests.

---
 .../java/ca/uhn/fhir/util/HapiExtensions.java |   6 +
 .../fhir/jpa/term/BaseTermReadSvcImpl.java    |   1 +
 ...irResourceDaoCreatePlaceholdersR4Test.java | 148 +++++++++++++++++-
 3 files changed, 153 insertions(+), 2 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
index 71b262f72f0..cd9028542ef 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
@@ -109,6 +109,12 @@ public class HapiExtensions {
 	/**
 	 * URL for boolean extension added to all placeholder resources
 	 */
+	public static final String EXT_RESOURCE_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-placeholder";
+
+	/**
+	 * URL for boolean extension added to all placeholder resources
+	 */
+	// FIXME: DM 2021-03-04 - This should probably be removed, and replaced with EXT_RESOURCE_PLACEHOLDER above
 	public static final String EXT_RESOURCE_META_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder";
 
 
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
index a5c579e096c..7c70a2d6129 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
@@ -2124,6 +2124,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	private boolean isPlaceholder(MetadataResource theResource) {
 		// FIXME: DM 2021-03-04 - We should probably check if this extension exists and the value is true.
+		// FIXME: DM 2021-03-04 - Don't like that getExtensionUrl returns null instead of empty collection.
 		return theResource.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER) != null;
 	}
 
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index 3b296bb9e68..cd7016121b7 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -7,9 +7,12 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.HapiExtensions;
 import com.google.common.collect.Sets;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.AuditEvent;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
@@ -26,6 +29,9 @@ import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
 @SuppressWarnings({"ConstantConditions"})
@@ -171,7 +177,96 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals("Patient/999999999999999", outcome.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless().getValue());
 	}
 
-	// FIXME: DM 2021-03-04 - These ARE the tests you're looking for.
+	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly
+	@Test
+	public void testCreatePlaceholderExtension_WithUpdateToTarget() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+
+		// Create an Observation that references a Patient
+		Observation obsToCreate = new Observation();
+		obsToCreate.setStatus(ObservationStatus.FINAL);
+		obsToCreate.getSubject().setReference("Patient/AAA");
+		IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
+
+		// Read the Observation
+		Observation createdObs = myObservationDao.read(id);
+		ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+
+		/*
+		 * Read the placeholder Patient referenced by the Observation
+		 * Placeholder extension should exist and be true
+		 */
+		Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
+		IIdType placeholderPatId = placeholderPat.getIdElement();
+		ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
+		assertEquals(0, placeholderPat.getIdentifier().size());
+		Extension extension = placeholderPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
+		assertNotNull(extension);
+		assertTrue(extension.hasValue());
+		assertTrue(((BooleanType) extension.getValue()).booleanValue());
+
+		// Update the Patient
+		Patient patToUpdate = new Patient();
+		patToUpdate.setId("Patient/AAA");
+		patToUpdate.addIdentifier().setSystem("http://foo").setValue("123");
+		IIdType updatedPatId = myPatientDao.update(patToUpdate).getId();
+
+		/*
+		 * Read the updated Patient
+		 * Placeholder extension should not exist
+		 */
+		Patient updatedPat = myPatientDao.read(updatedPatId);
+		ourLog.info("\nUpdated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedPat));
+		assertEquals(1, updatedPat.getIdentifier().size());
+		extension = updatedPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
+		assertNull(extension);
+	}
+
+	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly; probably shouldn't be in meta
+	@Test
+	public void testCreatePlaceholderMetaExtension_WithUpdateToTarget() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+
+		// Create an Observation that references a Patient
+		Observation obsToCreate = new Observation();
+		obsToCreate.setStatus(ObservationStatus.FINAL);
+		obsToCreate.getSubject().setReference("Patient/AAA");
+		IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
+
+		// Read the Observation
+		Observation createdObs = myObservationDao.read(id);
+		ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+
+		/*
+		 * Read the placeholder Patient referenced by the Observation
+		 * Placeholder extension should exist and be true
+		 */
+		Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
+		IIdType placeholderPatId = placeholderPat.getIdElement();
+		ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
+		assertEquals(0, placeholderPat.getIdentifier().size());
+		Extension extension = placeholderPat.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
+		assertNotNull(extension);
+		assertTrue(extension.hasValue());
+		assertTrue(((BooleanType) extension.getValue()).booleanValue());
+
+		// Update the Patient
+		Patient patToUpdate = new Patient();
+		patToUpdate.setId("Patient/AAA");
+		patToUpdate.addIdentifier().setSystem("http://foo").setValue("123");
+		IIdType updatedPatId = myPatientDao.update(patToUpdate).getId();
+
+		/*
+		 * Read the updated Patient
+		 * Placeholder extension should not exist
+		 */
+		Patient updatedPat = myPatientDao.read(updatedPatId);
+		ourLog.info("\nUpdated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedPat));
+		assertEquals(1, updatedPat.getIdentifier().size());
+		extension = updatedPat.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
+		assertNull(extension);
+	}
+
 	@Test
 	public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedByDefault() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
@@ -191,12 +286,61 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals(0, patient.getIdentifier().size());
 	}
 
+	// FIXME: DM 2021-03-04 - This test fails; placeholder identifier isn't populated by default
+	@Test
+	public void testCreatePlaceholderWithMatchUrl_PopulateIdentifierSetToDefault_WithUpdateToTarget() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+
+		/*
+		 * Create an Observation that references a Patient
+		 * Reference is populated with inline match URL and includes identifier
+		 */
+		Observation obsToCreate = new Observation();
+		obsToCreate.setStatus(ObservationStatus.FINAL);
+		obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123");
+		obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123");
+		IIdType obsId = myObservationDao.create(obsToCreate, mySrd).getId();
+
+		// Read the Observation
+		Observation createdObs = myObservationDao.read(obsId);
+		ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+
+		/*
+		 * Read the placeholder Patient referenced by the Observation
+		 * Identifier should be populated since it was provided
+		 */
+		Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
+		IIdType placeholderPatId = placeholderPat.getIdElement();
+		ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
+		assertEquals(1, placeholderPat.getIdentifier().size());
+		assertEquals(createdObs.getSubject().getReference(), placeholderPatId.toUnqualifiedVersionless().getValueAsString());
+
+		// Conditionally update a Patient with the same identifier
+		Patient patToConditionalUpdate = new Patient();
+		patToConditionalUpdate.addIdentifier().setSystem("http://foo").setValue("123");
+		patToConditionalUpdate.addName().setFamily("Simpson");
+		IIdType conditionalUpdatePatId = myPatientDao.update(patToConditionalUpdate, "Patient?identifier=http://foo|123", mySrd).getId();
+
+		// Read the conditionally updated Patient
+		Patient conditionalUpdatePat = myPatientDao.read(conditionalUpdatePatId);
+		ourLog.info("\nConditionally updated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conditionalUpdatePat));
+		assertEquals(1, conditionalUpdatePat.getIdentifier().size());
+
+		/*
+		 * Observation should reference conditionally updated Patient
+		 * ID of placeholder Patient should match ID of conditionally updated Patient
+		 */
+		createdObs = myObservationDao.read(obsId);
+		ourLog.info("\nObservation read after Patient update:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
+		assertEquals(createdObs.getSubject().getReference(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(placeholderPatId.toUnqualifiedVersionless().getValueAsString(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
+	}
 
 	@Test
 	public void testCreatePlaceholderWithMatchUrl_IdentifierCopied_NotPreExisting() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
-		// FIXME: DM - 2021-03-04 - Whaaat?! This is configurable. Awesome. What's the default?
 		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
 
 		Observation obsToCreate = new Observation();

From dfdcfa1365c398711dca0fd507dbce0866fe6ffe Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 17:01:39 -0500
Subject: [PATCH 04/13] Add failing tests.

---
 .../src/main/java/ca/uhn/fhir/util/HapiExtensions.java      | 2 +-
 .../ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java  | 1 +
 .../jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java | 6 +++---
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
index cd9028542ef..63121a0885d 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
@@ -114,7 +114,7 @@ public class HapiExtensions {
 	/**
 	 * URL for boolean extension added to all placeholder resources
 	 */
-	// FIXME: DM 2021-03-04 - This should probably be removed, and replaced with EXT_RESOURCE_PLACEHOLDER above
+	// FIXME: DM 2021-03-04 - This should probably be removed, and replaced with EXT_RESOURCE_PLACEHOLDER above.
 	public static final String EXT_RESOURCE_META_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder";
 
 
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
index f78746bbe6e..f453f3ce643 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
@@ -150,6 +150,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 		return Optional.ofNullable(valueOf);
 	}
 
+	// FIXME: DM 2021-03-04 - Should we throw an error if the identifier isn't available? Otherwise we get a placeholder with no identifier.
 	private <T extends IBaseResource> void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
 		boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
 		if (referenceHasIdentifier) {
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index cd7016121b7..820f5afe950 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -177,7 +177,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals("Patient/999999999999999", outcome.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless().getValue());
 	}
 
-	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly
+	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly.
 	@Test
 	public void testCreatePlaceholderExtension_WithUpdateToTarget() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
@@ -222,7 +222,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertNull(extension);
 	}
 
-	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly; probably shouldn't be in meta
+	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly; probably shouldn't be in meta.
 	@Test
 	public void testCreatePlaceholderMetaExtension_WithUpdateToTarget() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
@@ -286,7 +286,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals(0, patient.getIdentifier().size());
 	}
 
-	// FIXME: DM 2021-03-04 - This test fails; placeholder identifier isn't populated by default
+	// FIXME: DM 2021-03-04 - This test fails; placeholder identifier isn't populated by default.
 	@Test
 	public void testCreatePlaceholderWithMatchUrl_PopulateIdentifierSetToDefault_WithUpdateToTarget() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);

From 1d1d9a2f7c265ee7355114dca3a4bd99b2f88f7c Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 18:02:06 -0500
Subject: [PATCH 05/13] Fix typo in IGenericClient javadocs

---
 .../main/java/ca/uhn/fhir/rest/client/api/IGenericClient.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IGenericClient.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IGenericClient.java
index 03c79700423..56581458047 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IGenericClient.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IGenericClient.java
@@ -174,7 +174,7 @@ public interface IGenericClient extends IRestfulClient {
 	void unregisterInterceptor(Object theInterceptor);
 
 	/**
-	 * Fluent method for the "update" operation, which performs a logical delete on a server resource
+	 * Fluent method for the "update" operation, which updates a resource instance on the server
 	 */
 	IUpdate update();
 

From e3ba4bd1b61812867bbd872b84f2560a73a930f4 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 18:54:04 -0500
Subject: [PATCH 06/13] Set default for Populate Identifier in Auto-Created
 Placeholder Reference Targets to true; update javadocs accordingly

---
 .../java/ca/uhn/fhir/util/HapiExtensions.java |  3 +-
 .../ca/uhn/fhir/jpa/api/config/DaoConfig.java | 78 ++++++++++++++++++-
 ...irResourceDaoCreatePlaceholdersR4Test.java | 10 +--
 3 files changed, 81 insertions(+), 10 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
index 63121a0885d..3bd696d19f0 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
@@ -113,8 +113,9 @@ public class HapiExtensions {
 
 	/**
 	 * URL for boolean extension added to all placeholder resources
+	 *
+	 * @deprecated Deprecated in 5.4.0 in favour of {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER}
 	 */
-	// FIXME: DM 2021-03-04 - This should probably be removed, and replaced with EXT_RESOURCE_PLACEHOLDER above.
 	public static final String EXT_RESOURCE_META_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder";
 
 
diff --git a/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java b/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
index 25106646a56..c791f38fde5 100644
--- a/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
+++ b/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
@@ -186,9 +186,11 @@ public class DaoConfig {
 	private int myPreExpandValueSetsMaxCount = 1000;
 
 	/**
+	 * Do not change default of {@code true}!
+	 *
 	 * @since 4.2.0
 	 */
-	private boolean myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets;
+	private boolean myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets = true;
 
 	/**
 	 * @since 5.0.0
@@ -1102,7 +1104,7 @@ public class DaoConfig {
 
 	/**
 	 * When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this
-	 * setting is set to <code>true</code> (default is <code>false</code>) and the source
+	 * setting is set to <code>true</code> (default is <code>true</code>) and the source
 	 * reference has an identifier populated, the identifier will be copied to the target
 	 * resource.
 	 * <p>
@@ -1144,6 +1146,41 @@ public class DaoConfig {
 	 *   }
 	 * }
 	 * </pre>
+	 * <p>
+	 * Note that the default for this setting was previously <code>false</code>, and was changed to <code>true</code>
+	 * in 5.4.0 with consideration to the following:
+	 * </p>
+	 * <pre>
+	 * CP = Auto-Create Placeholder Reference Targets
+	 * PI = Populate Identifier in Auto-Created Placeholder Reference Targets
+	 *
+	 * CP | PI
+	 * -------
+	 *  F | F  <- PI=F is ignored
+	 *  F | T  <- PI=T is ignored
+	 *  T | F  <- resources may reference placeholder reference targets that are never updated : (
+	 *  T | T  <- placeholder reference targets can be updated : )
+	 * </pre>
+	 * <p>
+	 * Where CP=T and PI=F, the following could happen:
+	 * </p>
+	 * <ol>
+	 *    <li>
+	 *       Resource instance A is created with a reference to resource instance B. B is a placeholder reference target
+	 *       without an identifier.
+	 *    </li>
+	 *    <li>
+	 * 	   Resource instance C is conditionally created using a match URL. It is not matched to B although these
+	 * 	   resources represent the same entity.
+	 *    </li>
+	 *    <li>
+	 *       A continues to reference placeholder B, and does not reference populated C.
+	 *    </li>
+	 * </ol>
+	 * <p>
+	 * There may be cases where configuring this setting to <code>false</code> would be appropriate; however, these are
+	 * exceptional cases that should be opt-in.
+	 * </p>
 	 *
 	 * @since 4.2.0
 	 */
@@ -1153,7 +1190,7 @@ public class DaoConfig {
 
 	/**
 	 * When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this
-	 * setting is set to <code>true</code> (default is <code>false</code>) and the source
+	 * setting is set to <code>true</code> (default is <code>true</code>) and the source
 	 * reference has an identifier populated, the identifier will be copied to the target
 	 * resource.
 	 * <p>
@@ -1195,6 +1232,41 @@ public class DaoConfig {
 	 *   }
 	 * }
 	 * </pre>
+	 * <p>
+	 * Note that the default for this setting was previously <code>false</code>, and was changed to <code>true</code>
+	 * in 5.4.0 with consideration to the following:
+	 * </p>
+	 * <pre>
+	 * CP = Auto-Create Placeholder Reference Targets
+	 * PI = Populate Identifier in Auto-Created Placeholder Reference Targets
+	 *
+	 * CP | PI
+	 * -------
+	 *  F | F  <- PI=F is ignored
+	 *  F | T  <- PI=T is ignored
+	 *  T | F  <- resources may reference placeholder reference targets that are never updated : (
+	 *  T | T  <- placeholder reference targets can be updated : )
+	 * </pre>
+	 * <p>
+	 * Where CP=T and PI=F, the following could happen:
+	 * </p>
+	 * <ol>
+	 *    <li>
+	 *       Resource instance A is created with a reference to resource instance B. B is a placeholder reference target
+	 *       without an identifier.
+	 *    </li>
+	 *    <li>
+	 * 	   Resource instance C is conditionally created using a match URL. It is not matched to B although these
+	 * 	   resources represent the same entity.
+	 *    </li>
+	 *    <li>
+	 *       A continues to reference placeholder B, and does not reference populated C.
+	 *    </li>
+	 * </ol>
+	 * <p>
+	 * There may be cases where configuring this setting to <code>false</code> would be appropriate; however, these are
+	 * exceptional cases that should be opt-in.
+	 * </p>
 	 *
 	 * @since 4.2.0
 	 */
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index 820f5afe950..ae6a807fac1 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -268,9 +268,10 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedByDefault() {
+	public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopied() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(false);
 
 		Observation obsToCreate = new Observation();
 		obsToCreate.setStatus(ObservationStatus.FINAL);
@@ -288,7 +289,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 
 	// FIXME: DM 2021-03-04 - This test fails; placeholder identifier isn't populated by default.
 	@Test
-	public void testCreatePlaceholderWithMatchUrl_PopulateIdentifierSetToDefault_WithUpdateToTarget() {
+	public void testCreatePlaceholderWithMatchUrl_IdentifierCopiedByDefault_WithUpdateToTarget() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
 
@@ -338,10 +339,9 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testCreatePlaceholderWithMatchUrl_IdentifierCopied_NotPreExisting() {
+	public void testCreatePlaceholderWithMatchUrl_IdentifierCopiedByDefault_NotPreExisting() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
-		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
 
 		Observation obsToCreate = new Observation();
 		obsToCreate.setStatus(ObservationStatus.FINAL);
@@ -363,7 +363,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 	public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedBecauseNoFieldMatches() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
-		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
 		myDaoConfig.setBundleTypesAllowedForStorage(Sets.newHashSet(""));
 
 		AuditEvent eventToCreate = new AuditEvent();
@@ -382,7 +381,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 	public void testCreatePlaceholderWithMatchUrl_PreExisting() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
-		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
 
 		Patient patient = new Patient();
 		patient.setId("ABC");

From 96a21515429048b305cda2677e50d572bad6a8b7 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 19:19:34 -0500
Subject: [PATCH 07/13] Remove unnecessary FIXMEs.

---
 .../dao/index/SearchParamWithInlineReferencesExtractor.java    | 1 -
 .../main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java    | 1 -
 .../jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java    | 1 -
 .../src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java      | 3 ---
 4 files changed, 6 deletions(-)

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
index bdbf6ec991d..0a059bbc1ab 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
@@ -214,7 +214,6 @@ public class SearchParamWithInlineReferencesExtractor {
 	}
 
 
-	// FIXME: DM 2021-03-04 - This is where inline match URLs are handled.
 	/**
 	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
 	 * matching resource.
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
index 7c70a2d6129..a5c579e096c 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
@@ -2124,7 +2124,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	private boolean isPlaceholder(MetadataResource theResource) {
 		// FIXME: DM 2021-03-04 - We should probably check if this extension exists and the value is true.
-		// FIXME: DM 2021-03-04 - Don't like that getExtensionUrl returns null instead of empty collection.
 		return theResource.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER) != null;
 	}
 
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index ae6a807fac1..5392aad2bd4 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -287,7 +287,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals(0, patient.getIdentifier().size());
 	}
 
-	// FIXME: DM 2021-03-04 - This test fails; placeholder identifier isn't populated by default.
 	@Test
 	public void testCreatePlaceholderWithMatchUrl_IdentifierCopiedByDefault_WithUpdateToTarget() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
index 1f864c9471e..eeaa4eac020 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
@@ -357,9 +357,6 @@ public class NpmR4Test extends BaseJpaR4Test {
 		}
 	}
 
-	// FIXME: DM 2021-03-04 - This test is meant to validate that placeholder ValueSets are not created.
-	// FIXME: DM 2021-03-04 - This test or a new test should probably validate that placeholder ConceptMaps are also not created.
-	// FIXME: DM 2021-03-04 - This test does not validate that placeholder resources are created with a EXT_RESOURCE_META_PLACEHOLDER extension.
 	// Reproduces https://github.com/hapifhir/hapi-fhir/issues/2332
 	@Test
 	public void testInstallR4Package_AutoCreatePlaceholder() throws Exception {

From beab3522b9df8cca167836b5994ffd431d167102 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 19:33:00 -0500
Subject: [PATCH 08/13] Enhance isPlaceholder to check value of placeholder
 extension.

---
 .../jpa/dao/index/DaoResourceLinkResolver.java     |  3 +--
 .../ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java  | 14 ++++++++++----
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
index f453f3ce643..0faaa9eb160 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
@@ -110,7 +110,6 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 		return resolvedResource;
 	}
 
-	// FIXME: DM 2021-03-04 - This is where placeholder reference targets are handled.
 	/**
 	 * @param theIdToAssignToPlaceholder If specified, the placeholder resource created will be given a specific ID
 	 */
@@ -150,7 +149,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 		return Optional.ofNullable(valueOf);
 	}
 
-	// FIXME: DM 2021-03-04 - Should we throw an error if the identifier isn't available? Otherwise we get a placeholder with no identifier.
+	// FIXME: DM 2021-03-04 - Should we issue a warning if the identifier isn't available?
 	private <T extends IBaseResource> void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
 		boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
 		if (referenceHasIdentifier) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
index a5c579e096c..0a8d646a9bb 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
@@ -119,15 +119,17 @@ import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.DomainResource;
 import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.IntegerType;
-import org.hl7.fhir.r4.model.MetadataResource;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
@@ -2122,9 +2124,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		}
 	}
 
-	private boolean isPlaceholder(MetadataResource theResource) {
-		// FIXME: DM 2021-03-04 - We should probably check if this extension exists and the value is true.
-		return theResource.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER) != null;
+	private boolean isPlaceholder(DomainResource theResource) {
+		boolean retVal = false;
+		Extension extension = theResource.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
+		if (extension != null && extension.hasValue() && extension.getValue() instanceof BooleanType) {
+			retVal = ((BooleanType) extension.getValue()).booleanValue();
+		}
+		return retVal;
 	}
 
 	@Override

From bd85c0c36233469bd591d491bd8fac965ac4ef27 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 19:38:09 -0500
Subject: [PATCH 09/13] Remove unnecessary failing test.

---
 ...irResourceDaoCreatePlaceholdersR4Test.java | 47 +------------------
 1 file changed, 1 insertion(+), 46 deletions(-)

diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index 5392aad2bd4..a81f245578a 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -201,7 +201,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
 		assertEquals(0, placeholderPat.getIdentifier().size());
 		Extension extension = placeholderPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
-		assertNotNull(extension);
+		assertNotNull(extension); // FIXME: DM 2021-03-04 - This assertion fails for now.
 		assertTrue(extension.hasValue());
 		assertTrue(((BooleanType) extension.getValue()).booleanValue());
 
@@ -222,51 +222,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertNull(extension);
 	}
 
-	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly; probably shouldn't be in meta.
-	@Test
-	public void testCreatePlaceholderMetaExtension_WithUpdateToTarget() {
-		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
-
-		// Create an Observation that references a Patient
-		Observation obsToCreate = new Observation();
-		obsToCreate.setStatus(ObservationStatus.FINAL);
-		obsToCreate.getSubject().setReference("Patient/AAA");
-		IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
-
-		// Read the Observation
-		Observation createdObs = myObservationDao.read(id);
-		ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
-
-		/*
-		 * Read the placeholder Patient referenced by the Observation
-		 * Placeholder extension should exist and be true
-		 */
-		Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
-		IIdType placeholderPatId = placeholderPat.getIdElement();
-		ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
-		assertEquals(0, placeholderPat.getIdentifier().size());
-		Extension extension = placeholderPat.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
-		assertNotNull(extension);
-		assertTrue(extension.hasValue());
-		assertTrue(((BooleanType) extension.getValue()).booleanValue());
-
-		// Update the Patient
-		Patient patToUpdate = new Patient();
-		patToUpdate.setId("Patient/AAA");
-		patToUpdate.addIdentifier().setSystem("http://foo").setValue("123");
-		IIdType updatedPatId = myPatientDao.update(patToUpdate).getId();
-
-		/*
-		 * Read the updated Patient
-		 * Placeholder extension should not exist
-		 */
-		Patient updatedPat = myPatientDao.read(updatedPatId);
-		ourLog.info("\nUpdated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedPat));
-		assertEquals(1, updatedPat.getIdentifier().size());
-		extension = updatedPat.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
-		assertNull(extension);
-	}
-
 	@Test
 	public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopied() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);

From 35645999d7dac4f30ac0dc146daa8e7686211d78 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Thu, 4 Mar 2021 19:55:39 -0500
Subject: [PATCH 10/13] Add changelog entries.

---
 .../2332-placeholder-valuset-skips-terminology-storage.yaml  | 3 +--
 ...ce-targets-need-to-be-resolved-placeholder-extension.yaml | 5 +++++
 ...gets-need-to-be-resolved-placeholder-identifier-true.yaml | 5 +++++
 3 files changed, 11 insertions(+), 2 deletions(-)
 create mode 100644 hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-extension.yaml
 create mode 100644 hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-identifier-true.yaml

diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2332-placeholder-valuset-skips-terminology-storage.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2332-placeholder-valuset-skips-terminology-storage.yaml
index cfde3b592df..8a63c1340a5 100644
--- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2332-placeholder-valuset-skips-terminology-storage.yaml
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2332-placeholder-valuset-skips-terminology-storage.yaml
@@ -1,5 +1,4 @@
 ---
 type: add
 issue: 2332
-title: "All created placeholder resources now have a meta extension with the url http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder
- and the value 'true'.  Also, terminology storage is now skipped for placeholder ValueSet and ConceptMap resources."
+title: "Terminology storage is now skipped for placeholder ValueSet and ConceptMap resources."
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-extension.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-extension.yaml
new file mode 100644
index 00000000000..849ebfd76a1
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-extension.yaml
@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2446
+title: "Auto-created placeholder reference targets now have an extension with the URL
+   `http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder` and a value of `true`."
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-identifier-true.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-identifier-true.yaml
new file mode 100644
index 00000000000..47398526684
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2446-issues-with-placeholder-reference-targets-need-to-be-resolved-placeholder-identifier-true.yaml
@@ -0,0 +1,5 @@
+---
+type: change
+issue: 2446
+title: "DaoConfig setting for [Populate Identifier In Auto Created Placeholder Reference Targets](https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean))
+   now defaults to `true`."

From a195eebdecc1a97c85242e3ace179eef64eedbdc Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Fri, 5 Mar 2021 12:09:17 -0500
Subject: [PATCH 11/13] Placeholder extension moved to resource body from meta;
 tests passing.

---
 .../main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java  | 4 ++--
 .../uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java  | 9 +++------
 .../dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java  | 3 +--
 3 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java b/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
index c791f38fde5..def5d13846f 100644
--- a/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
+++ b/hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
@@ -1071,7 +1071,7 @@ public class DaoConfig {
 	 * as they are never allowed to be client supplied in HAPI FHIR JPA.
 	 *
 	 * All placeholder resources created in this way have a meta extension
-	 * with the URL {@link HapiExtensions#EXT_RESOURCE_META_PLACEHOLDER} and the value "true".
+	 * with the URL {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER} and the value "true".
 	 * </p>
 	 */
 	public boolean isAutoCreatePlaceholderReferenceTargets() {
@@ -1095,7 +1095,7 @@ public class DaoConfig {
 	 * as they are never allowed to be client supplied in HAPI FHIR JPA.
 	 *
 	 * All placeholder resources created in this way have a meta extension
-	 * with the URL {@link HapiExtensions#EXT_RESOURCE_META_PLACEHOLDER} and the value "true".
+	 * with the URL {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER} and the value "true".
 	 * </p>
 	 */
 	public void setAutoCreatePlaceholderReferenceTargets(boolean theAutoCreatePlaceholderReferenceTargets) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
index 0faaa9eb160..2c0d06dfebc 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
@@ -41,7 +41,6 @@ import ca.uhn.fhir.util.HapiExtensions;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
-import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -123,11 +122,9 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 			@SuppressWarnings("unchecked")
 			T newResource = (T) missingResourceDef.newInstance();
 
-			// FIXME: DM 2021-03-04 - This is where the placeholder extension is added; should be in resource body instead of meta?
-			IBaseMetaType meta = newResource.getMeta();
-			if (meta instanceof IBaseHasExtensions) {
-				IBaseExtension<?, ?> extension = ((IBaseHasExtensions) meta).addExtension();
-				extension.setUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
+			if (newResource instanceof IBaseHasExtensions) {
+				IBaseExtension<?, ?> extension = ((IBaseHasExtensions) newResource).addExtension();
+				extension.setUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
 				extension.setValue(myContext.getPrimitiveBoolean(true));
 			}
 
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
index a81f245578a..badb1502a49 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
@@ -177,7 +177,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		assertEquals("Patient/999999999999999", outcome.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless().getValue());
 	}
 
-	// FIXME: DM 2021-03-04 - This test fails; extension isn't being created correctly.
 	@Test
 	public void testCreatePlaceholderExtension_WithUpdateToTarget() {
 		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
@@ -201,7 +200,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
 		assertEquals(0, placeholderPat.getIdentifier().size());
 		Extension extension = placeholderPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
-		assertNotNull(extension); // FIXME: DM 2021-03-04 - This assertion fails for now.
+		assertNotNull(extension);
 		assertTrue(extension.hasValue());
 		assertTrue(((BooleanType) extension.getValue()).booleanValue());
 

From 2945cd9f748a99a187cb0022619d286479234d1e Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Fri, 5 Mar 2021 12:33:23 -0500
Subject: [PATCH 12/13] Remove FIXME

---
 .../java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
index 2c0d06dfebc..fe3f0d0c6d9 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
@@ -146,7 +146,6 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 		return Optional.ofNullable(valueOf);
 	}
 
-	// FIXME: DM 2021-03-04 - Should we issue a warning if the identifier isn't available?
 	private <T extends IBaseResource> void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
 		boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
 		if (referenceHasIdentifier) {

From 214c7eb45e78d7378f93c36234c87e1672757370 Mon Sep 17 00:00:00 2001
From: Diederik Muylwyk <diederik.muylwyk@gmail.com>
Date: Fri, 5 Mar 2021 12:59:26 -0500
Subject: [PATCH 13/13] Remove unnecessary field.

---
 .../src/main/java/ca/uhn/fhir/util/HapiExtensions.java    | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
index 3bd696d19f0..3d5d052ac78 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
@@ -111,14 +111,6 @@ public class HapiExtensions {
 	 */
 	public static final String EXT_RESOURCE_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-placeholder";
 
-	/**
-	 * URL for boolean extension added to all placeholder resources
-	 *
-	 * @deprecated Deprecated in 5.4.0 in favour of {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER}
-	 */
-	public static final String EXT_RESOURCE_META_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder";
-
-
 	/**
 	 * Non instantiable
 	 */