Descendent fix (#5669)

* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>

* pom bump, doc add, version enum add (#5616)

Co-authored-by: Long Ma <long@smilecdr.com>

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5603-is-a-descendent-of.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5603
+jira: SMILE-8000
+title: "Previously, the semantics of `is-a` were incorrect in Valueset Expansion. The implementation previously used the behaviour of `descendent-of`, which means that `A is-a A` was not being considered as true. This has been corrected. In addition, 
+`descendent-of` is now supported, which compares for strict descendency, and does not include itself. Thanks to Ole Hedegaard (@ohetrifork) for the fix."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-05-18"
+codename: "Borealis"

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java

@@ -1598,6 +1598,16 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		TermConcept code = findCodeForFilterCriteria(theSystem, theFilter);
 
 		if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
+			ourLog.debug(
+					" * Filtering on specific code and codes with a parent of {}/{}/{}",
+					code.getId(),
+					code.getCode(),
+					code.getDisplay());
+
+			b.must(f.bool()
+					.should(f.match().field("myParentPids").matching("" + code.getId()))
+					.should(f.match().field("myId").matching(code.getId())));
+		} else if (theFilter.getOp() == ValueSet.FilterOperator.DESCENDENTOF) {
 			ourLog.debug(
 					" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
 

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java

@@ -786,7 +786,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest impl
 		logAndValidateValueSet(result);
 
 		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
-		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
+		assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
 	}
 
 	@Test

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -313,7 +313,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 			.setSystem(codeSystem.getUrl())
 			.addFilter()
 			.setProperty("concept")
-			.setOp(FilterOperator.ISA)
+			.setOp(FilterOperator.DESCENDENTOF)
 			.setValue("dogs");
 
 		myValueSetDao.create(valueSet, mySrd);
@@ -504,7 +504,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		logAndValidateValueSet(result);
 
 		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
-		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
+		assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
 
 	}
 
@@ -535,7 +535,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		logAndValidateValueSet(result);
 
 		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
-		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
+		assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
 
 	}
 
@@ -650,7 +650,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		ValueSet vs = new ValueSet();
 		ConceptSetComponent include = vs.getCompose().addInclude();
 		include.setSystem(URL_MY_CODE_SYSTEM);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 
 		ValueSet result = myValueSetDao.expand(vs, null);
 		logAndValidateValueSet(result);
@@ -669,7 +669,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		vs = new ValueSet();
 		include = vs.getCompose().addInclude();
 		include.setSystem(URL_MY_CODE_SYSTEM);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		result = myValueSetDao.expand(vs, null);
 		logAndValidateValueSet(result);
 

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetVersionedTest.java

@@ -230,7 +230,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
 		include.setSystem(theCodeSystemUrl);
 		include.setVersion(theValueSetVersion);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		return myLocalVs;
 
 	}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java

@@ -353,7 +353,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 			.setSystem(codeSystem.getUrl())
 			.addFilter()
 			.setProperty("concept")
-			.setOp(FilterOperator.ISA)
+			.setOp(FilterOperator.DESCENDENTOF)
 			.setValue("dogs");
 
 		myValueSetDao.create(valueSet, mySrd);
@@ -584,7 +584,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		logAndValidateValueSet(result);
 
 		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
-		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
+		assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
 
 	}
 
@@ -610,6 +610,34 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		logAndValidateValueSet(result);
 
 		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
+		assertEquals(3, codes.size());
+		assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
+
+	}
+
+	@Test
+	public void testExpandWithDescendentOfInExternalValueSetReindex() {
+		TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
+
+		createExternalCsAndLocalVs();
+
+		myResourceReindexingSvc.markAllResourcesForReindexing();
+		myResourceReindexingSvc.forceReindexingPass();
+		myResourceReindexingSvc.forceReindexingPass();
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myTerminologyDeferredStorageSvc.saveDeferred();
+
+		ValueSet vs = new ValueSet();
+		ConceptSetComponent include = vs.getCompose().addInclude();
+		include.setSystem(TermTestUtil.URL_MY_CODE_SYSTEM);
+		include.addFilter().setOp(FilterOperator.DESCENDENTOF).setValue("childAA").setProperty("concept");
+
+		ValueSet result = myValueSetDao.expand(vs, null); // breakpoint
+		logAndValidateValueSet(result);
+
+		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
+		assertEquals(2, codes.size());
 		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
 
 	}
@@ -795,7 +823,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		ValueSet vs = new ValueSet();
 		ConceptSetComponent include = vs.getCompose().addInclude();
 		include.setSystem(TermTestUtil.URL_MY_CODE_SYSTEM);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 
 		ValueSet result = myValueSetDao.expand(vs, null);
 		logAndValidateValueSet(result);
@@ -814,7 +842,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
 		vs = new ValueSet();
 		include = vs.getCompose().addInclude();
 		include.setSystem(TermTestUtil.URL_MY_CODE_SYSTEM);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		result = myValueSetDao.expand(vs, null);
 		logAndValidateValueSet(result);
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetNoVerCSNoVerTest.java

@@ -202,7 +202,7 @@ public class ResourceProviderR4ValueSetNoVerCSNoVerTest extends BaseResourceProv
 		myLocalVs.setUrl(URL_MY_VALUE_SET);
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
 		include.setSystem(codeSystem.getUrl());
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
 	}
 
@@ -1199,7 +1199,7 @@ public class ResourceProviderR4ValueSetNoVerCSNoVerTest extends BaseResourceProv
 			.setSystem(URL_MY_CODE_SYSTEM)
 			.addFilter()
 			.setProperty("concept")
-			.setOp(FilterOperator.ISA)
+			.setOp(FilterOperator.DESCENDENTOF)
 			.setValue("A");
 		myLocalVs
 			.getCompose()

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetVerCSNoVerTest.java

@@ -167,7 +167,7 @@ public class ResourceProviderR4ValueSetVerCSNoVerTest extends BaseResourceProvid
 		myLocalVs.setUrl(URL_MY_VALUE_SET);
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
 		include.setSystem(codeSystem.getUrl());
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
 	}
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetVerCSVerTest.java

@@ -196,7 +196,7 @@ public class ResourceProviderR4ValueSetVerCSVerTest extends BaseResourceProvider
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
 		include.setSystem(theCodeSystemUrl);
 		include.setVersion(theValueSetVersion);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		return myLocalVs;
 
 	}

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java

@@ -208,7 +208,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
 		myLocalVs.setUrl(URL_MY_VALUE_SET);
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
 		include.setSystem(codeSystem.getUrl());
-		include.addFilter().setProperty("concept").setOp(Enumerations.FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(Enumerations.FilterOperator.DESCENDENTOF).setValue("ParentA");
 		myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
 	}
 

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetVersionedTest.java

@@ -231,7 +231,7 @@ public class ResourceProviderR5ValueSetVersionedTest extends BaseResourceProvide
 		ConceptSetComponent include = myLocalVs.getCompose().addInclude();
 		include.setSystem(theCodeSystemUrl);
 		include.setVersion(theValueSetVersion);
-		include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
+		include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
 		return myLocalVs;
 
 	}

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/channel/api/BaseChannelSettings.java

@@ -26,6 +26,9 @@ public abstract class BaseChannelSettings implements IChannelSettings {
 
 	private ChannelRetryConfiguration myRetryConfigurationParameters;
 
+	// init true to match previous behaviour
+	private boolean myUseJacksonMessageConverter = true;
+
 	/**
 	 * Default true.  Used by IChannelNamer to decide how to qualify the channel name.
 	 */