Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir

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

@@ -63,6 +63,7 @@ public enum VersionEnum {
 	V4_3_0, // 4.3.0 was renamed to 5.0.0 during the cycle
 	V5_0_0,
 	V5_0_1,
+	V5_0_2,
 	V5_1_0;
 
 	public static VersionEnum latestVersion() {

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_0_2/changes.yaml

@@ -0,0 +1,11 @@
+---
+- item:
+    type: "add"
+    title: "This release corrects a snapshot dependency on org.hl7.fhir.core that was accidentally
+    left in HAPI FHIR 5.0.1."
+- item:
+     type: "change"
+     title: "The default setting for the partition mode's Include Hashes in Search Indexes setting was
+   incorrectly set to true in HAPI FHIR 5.0.0 and has now been changed to false, as this is a more sensible
+   default. Note that this wil affect existing systems that are trying this feature out. A manual reindex of
+   data may be required."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_0_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2020-06-02"
+codename: "Labrador"

hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/svc/EmpiPersonMergerSvcTest.java

@@ -28,6 +28,7 @@ import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
 
+import static org.hamcrest.Matchers.hasSize;
 import static org.hamcrest.Matchers.is;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
@@ -315,6 +316,55 @@ public class EmpiPersonMergerSvcTest extends BaseEmpiR4Test {
 		assertEquals(3, myKeepPerson.getLink().size());
 	}
 
+	@Test
+	public void testMergeNames() {
+		myDeletePerson.addName().addGiven("Jim");
+		myDeletePerson.getNameFirstRep().addGiven("George");
+		assertThat(myDeletePerson.getName(), hasSize(1));
+		assertThat(myDeletePerson.getName().get(0).getGiven(), hasSize(2));
+
+		myKeepPerson.addName().addGiven("Jeff");
+		myKeepPerson.getNameFirstRep().addGiven("George");
+		assertThat(myKeepPerson.getName(), hasSize(1));
+		assertThat(myKeepPerson.getName().get(0).getGiven(), hasSize(2));
+
+		mergePersons();
+		assertThat(myKeepPerson.getName(), hasSize(2));
+		assertThat(myKeepPerson.getName().get(0).getGiven(), hasSize(2));
+		assertThat(myKeepPerson.getName().get(1).getGiven(), hasSize(2));
+	}
+
+	@Test
+	public void testMergeNamesAllSame() {
+		myDeletePerson.addName().addGiven("Jim");
+		myDeletePerson.getNameFirstRep().addGiven("George");
+		assertThat(myDeletePerson.getName(), hasSize(1));
+		assertThat(myDeletePerson.getName().get(0).getGiven(), hasSize(2));
+
+		myKeepPerson.addName().addGiven("Jim");
+		myKeepPerson.getNameFirstRep().addGiven("George");
+		assertThat(myKeepPerson.getName(), hasSize(1));
+		assertThat(myKeepPerson.getName().get(0).getGiven(), hasSize(2));
+
+		mergePersons();
+		assertThat(myKeepPerson.getName(), hasSize(1));
+		assertThat(myKeepPerson.getName().get(0).getGiven(), hasSize(2));
+	}
+
+	@Test
+	public void testMergeIdentities() {
+		myDeletePerson.addIdentifier().setValue("aaa");
+		myDeletePerson.addIdentifier().setValue("bbb");
+		assertThat(myDeletePerson.getIdentifier(), hasSize(2));
+
+		myKeepPerson.addIdentifier().setValue("aaa");
+		myKeepPerson.addIdentifier().setValue("ccc");
+		assertThat(myKeepPerson.getIdentifier(), hasSize(2));
+
+		mergePersons();
+		assertThat(myKeepPerson.getIdentifier(), hasSize(3));
+	}
+
 	private EmpiLink createEmpiLink(Person thePerson, Patient theTargetPatient) {
 		thePerson.addLink().setTarget(new Reference(theTargetPatient));
 		return myEmpiLinkDaoSvc.createOrUpdateLinkEntity(thePerson, theTargetPatient, EmpiMatchResultEnum.POSSIBLE_MATCH, EmpiLinkSourceEnum.AUTO, createContextForCreate());

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/config/PartitionSettings.java

@@ -27,10 +27,10 @@ public class PartitionSettings {
 
 	private boolean myPartitioningEnabled = false;
 	private CrossPartitionReferenceMode myAllowReferencesAcrossPartitions = CrossPartitionReferenceMode.NOT_ALLOWED;
-	private boolean myIncludePartitionInSearchHashes = true;
+	private boolean myIncludePartitionInSearchHashes = false;
 
 	/**
-	 * If set to <code>true</code> (default is <code>true</code>) the <code>PARTITION_ID</code> value will be factored into the
+	 * If set to <code>true</code> (default is <code>false</code>) the <code>PARTITION_ID</code> value will be factored into the
 	 * hash values used in the <code>HFJ_SPIDX_xxx</code> tables, removing the need to explicitly add a selector
 	 * on this column in queries. If set to <code>false</code>, an additional selector is used instead, which may perform
 	 * better when using native database partitioning features.
@@ -43,7 +43,7 @@ public class PartitionSettings {
 	}
 
 	/**
-	 * If set to <code>true</code> (default is <code>true</code>) the <code>PARTITION_ID</code> value will be factored into the
+	 * If set to <code>true</code> (default is <code>false</code>) the <code>PARTITION_ID</code> value will be factored into the
 	 * hash values used in the <code>HFJ_SPIDX_xxx</code> tables, removing the need to explicitly add a selector
 	 * on this column in queries. If set to <code>false</code>, an additional selector is used instead, which may perform
 	 * better when using native database partitioning features.

hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/util/PersonHelper.java

@@ -34,7 +34,10 @@ import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Address;
 import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.ContactPoint;
+import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Person;
@@ -45,8 +48,11 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Nonnull;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
+import java.util.function.BiPredicate;
+import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -476,15 +482,11 @@ public class PersonHelper {
 	private void mergeR4PersonFields(IBaseResource thePersonToDelete, IBaseResource thePersonToKeep) {
 		Person fromPerson = (Person) thePersonToDelete;
 		Person toPerson = (Person) thePersonToKeep;
-		if (!toPerson.hasName()) {
+
-			toPerson.setName(fromPerson.getName());
+		mergeElementList(fromPerson, toPerson, HumanName.class, Person::getName, HumanName::equalsDeep);
-		}
+		mergeElementList(fromPerson, toPerson, Identifier.class, Person::getIdentifier, Identifier::equalsDeep);
-		if (!toPerson.hasAddress()) {
+		mergeElementList(fromPerson, toPerson, Address.class, Person::getAddress, Address::equalsDeep);
-			toPerson.setAddress(fromPerson.getAddress());
+		mergeElementList(fromPerson, toPerson, ContactPoint.class, Person::getTelecom, ContactPoint::equalsDeep);
-		}
-		if (!toPerson.hasTelecom()) {
-			toPerson.setTelecom(fromPerson.getTelecom());
-		}
 		if (!toPerson.hasBirthDate()) {
 			toPerson.setBirthDate(fromPerson.getBirthDate());
 		}
@@ -496,19 +498,28 @@ public class PersonHelper {
 		}
 	}
 
+	private <P,T> void mergeElementList(P fromPerson, P toPerson, Class<T> theBase, Function<P, List<T>> theGetList, BiPredicate<T, T> theEquals) {
+		List<T> fromList = theGetList.apply(fromPerson);
+		List<T> toList = theGetList.apply(toPerson);
+		List<T> itemsToAdd = new ArrayList<>();
+
+		for (T fromItem : fromList) {
+			if (toList.stream().noneMatch(t -> theEquals.test(fromItem, t))) {
+				itemsToAdd.add(fromItem);
+			}
+		}
+		toList.addAll(itemsToAdd);
+	}
 
 	private void mergeDstu3PersonFields(IBaseResource thePersonToDelete, IBaseResource thePersonToKeep) {
 		org.hl7.fhir.dstu3.model.Person fromPerson = (org.hl7.fhir.dstu3.model.Person) thePersonToDelete;
 		org.hl7.fhir.dstu3.model.Person toPerson = (org.hl7.fhir.dstu3.model.Person) thePersonToKeep;
-		if (!toPerson.hasName()) {
+
-			toPerson.setName(fromPerson.getName());
+		mergeElementList(fromPerson, toPerson, org.hl7.fhir.dstu3.model.HumanName.class, org.hl7.fhir.dstu3.model.Person::getName, org.hl7.fhir.dstu3.model.HumanName::equalsDeep);
-		}
+		mergeElementList(fromPerson, toPerson, org.hl7.fhir.dstu3.model.Identifier.class, org.hl7.fhir.dstu3.model.Person::getIdentifier, org.hl7.fhir.dstu3.model.Identifier::equalsDeep);
-		if (!toPerson.hasAddress()) {
+		mergeElementList(fromPerson, toPerson, org.hl7.fhir.dstu3.model.Address.class, org.hl7.fhir.dstu3.model.Person::getAddress, org.hl7.fhir.dstu3.model.Address::equalsDeep);
-			toPerson.setAddress(fromPerson.getAddress());
+		mergeElementList(fromPerson, toPerson, org.hl7.fhir.dstu3.model.ContactPoint.class, org.hl7.fhir.dstu3.model.Person::getTelecom, org.hl7.fhir.dstu3.model.ContactPoint::equalsDeep);
-		}
+
-		if (!toPerson.hasTelecom()) {
-			toPerson.setTelecom(fromPerson.getTelecom());
-		}
 		if (!toPerson.hasBirthDate()) {
 			toPerson.setBirthDate(fromPerson.getBirthDate());
 		}