Correctly Expand ValueSets in non-lucene mode (#1573)

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

@@ -424,13 +424,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 	private void logConceptsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theConceptsExpanded) {
 		if (theConceptsExpanded > 0) {
-			ourLog.info("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theTermValueSet.getUrl());
+			ourLog.debug("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theTermValueSet.getUrl());
 		}
 	}
 
 	private void logDesignationsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theDesignationsExpanded) {
 		if (theDesignationsExpanded > 0) {
-			ourLog.info("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theTermValueSet.getUrl());
+			ourLog.debug("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theTermValueSet.getUrl());
 		}
 	}
 
@@ -446,7 +446,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 		StopWatch sw = new StopWatch();
 		String valueSetInfo = getValueSetInfo(theValueSetToExpand);
-		ourLog.info("Working with {}", valueSetInfo);
+		ourLog.debug("Working with {}", valueSetInfo);
 
 		// Handle includes
 		ourLog.debug("Handling includes");
@@ -488,7 +488,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 			myTxTemplate.execute(t -> ((ValueSetConceptAccumulator) theValueSetCodeAccumulator).removeGapsFromConceptOrder());
 		}
 
-		ourLog.info("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
+		ourLog.debug("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
 	}
 
 	private String getValueSetInfo(ValueSet theValueSet) {
@@ -553,7 +553,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 				return false;
 			}
 
-			ourLog.info("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
+			ourLog.debug("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
 
 			TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
 			if (cs != null) {
@@ -566,7 +566,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 				 * since we're going to do it without the database.
 				 */
 				if (myFulltextSearchSvc == null) {
-					expandWithoutHibernateSearch(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, system, theAdd, theCodeCounter);
+					expandWithoutHibernateSearch(theValueSetCodeAccumulator, csv, theAddedCodes, theIncludeOrExclude, system, theAdd, theCodeCounter);
 					return false;
 				}
 
@@ -642,7 +642,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 				jpaQuery.setMaxResults(maxResultsPerBatch);
 				jpaQuery.setFirstResult(theQueryIndex * maxResultsPerBatch);
 
-				ourLog.info("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
+				ourLog.debug("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
 
 				StopWatch swForBatch = new StopWatch();
 				AtomicInteger countForBatch = new AtomicInteger(0);
@@ -661,10 +661,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 					}
 				}
 
-				ourLog.info("Batch expansion for {} with starting index of {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), firstResult, countForBatch, swForBatch.getMillis());
+				ourLog.debug("Batch expansion for {} with starting index of {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), firstResult, countForBatch, swForBatch.getMillis());
 
 				if (resultsInBatch < maxResultsPerBatch) {
-					ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
+					ourLog.debug("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
 					return false;
 				} else {
 					return true;
@@ -712,7 +712,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		} else if (hasValueSet) {
 
 			for (CanonicalType nextValueSet : theIncludeOrExclude.getValueSet()) {
-				ourLog.info("Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
+				ourLog.debug("Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
 
 				List<VersionIndependentConcept> expanded = expandValueSet(nextValueSet.getValueAsString());
 				Map<String, TermCodeSystem> uriToCodeSystem = new HashMap<>();
@@ -848,7 +848,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 			.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + theSystem + "}" + theFilter.getValue()));
 
 		if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
-			ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
+			ourLog.debug(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
 			theBool.must(theQb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
 		} else {
 			throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
@@ -1015,7 +1015,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 	}
 
 	private void logFilteringValueOnProperty(String theValue, String theProperty) {
-		ourLog.info(" * Filtering with value={} on property {}", theValue, theProperty);
+		ourLog.debug(" * Filtering with value={} on property {}", theValue, theProperty);
 	}
 
 	private void throwInvalidRequestForOpOnProperty(ValueSet.FilterOperator theOp, String theProperty) {
@@ -1060,7 +1060,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		}
 	}
 
-	private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
+	private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, TermCodeSystemVersion theVersion, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
 		ourLog.trace("Hibernate search is not enabled");
 		if (theValueSetCodeAccumulator instanceof ValueSetExpansionComponentWithConceptAccumulator) {
 			Validate.isTrue(((ValueSetExpansionComponentWithConceptAccumulator) theValueSetCodeAccumulator).getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
@@ -1068,12 +1068,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 		Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
 		Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
 
+
+		if (theInclude.getConcept().isEmpty()) {
+			for (TermConcept next : theVersion.getConcepts()) {
+				addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, null, theAdd, theCodeCounter, theSystem, next.getCode(), next.getDisplay());
+			}
+		}
+
 		for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
 			if (!theSystem.equals(theInclude.getSystem())) {
 				continue;
 			}
 			addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, null, theAdd, theCodeCounter, theSystem, next.getCode(), next.getDisplay());
 		}
+
+
 	}
 
 	@Override
@@ -1215,7 +1224,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 		fetchParents(concept.get(), retVal);
 
-		ourLog.info("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.getMillis());
+		ourLog.debug("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.getMillis());
 		return retVal;
 	}
 
@@ -1246,7 +1255,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 		fetchChildren(concept.get(), retVal);
 
-		ourLog.info("Fetched {} codes below code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
+		ourLog.debug("Fetched {} codes below code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
 		return retVal;
 	}
 
@@ -1295,7 +1304,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 	@Override
 	@Transactional
 	public void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap) {
-		ourLog.info("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
+		ourLog.debug("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
 		ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theConceptMap.getUrl(), "ConceptMap has no value for ConceptMap.url");

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

@@ -335,7 +335,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 				populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
 
 				persCs.getConcepts().addAll(BaseTermReadSvcImpl.toPersistedConcepts(theCodeSystem.getConcept(), persCs));
-				ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
+				ourLog.debug("Code system has {} concepts", persCs.getConcepts().size());
 				storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs, theResourceEntity);
 			}
 
@@ -366,7 +366,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
 	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
-		ourLog.info("Storing code system");
+		ourLog.debug("Storing code system");
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
@@ -378,15 +378,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		 * For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
 		 */
 
-		ourLog.info("Deleting old code system versions");
 		for (TermCodeSystemVersion next : existing) {
+			ourLog.info("Deleting old code system version {}", next.getPid());
 			Long codeSystemVersionPid = next.getPid();
 			deleteCodeSystemVersion(codeSystemVersionPid);
 		}
 
-		ourLog.info("Flushing...");
+		ourLog.debug("Flushing...");
 		myConceptDao.flush();
-		ourLog.info("Done flushing");
+		ourLog.debug("Done flushing");
 
 		/*
 		 * Do the upload
@@ -399,7 +399,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
 		theCodeSystemVersion.setCodeSystemVersionId(theSystemVersionId);
 
-		ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
+		ourLog.debug("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
 
 		// Validate the code system
 		ArrayList<String> conceptsStack = new ArrayList<>();
@@ -409,35 +409,33 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
 		}
 
-		ourLog.info("Saving version containing {} concepts", totalCodeCount);
+		ourLog.debug("Saving version containing {} concepts", totalCodeCount);
 
 		TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
 
-		ourLog.info("Saving code system");
+		ourLog.debug("Saving code system");
 
 		codeSystem.setCurrentVersion(theCodeSystemVersion);
 		codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
 
-		ourLog.info("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
+		ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
 
 		for (TermConcept next : theCodeSystemVersion.getConcepts()) {
 			populateVersion(next, codeSystemVersion);
 		}
 
-		ourLog.info("Saving {} concepts...", totalCodeCount);
+		ourLog.debug("Saving {} concepts...", totalCodeCount);
 
 		IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
 		for (TermConcept next : theCodeSystemVersion.getConcepts()) {
 			persistChildren(next, codeSystemVersion, conceptsStack2, totalCodeCount);
 		}
 
-		ourLog.info("Done saving concepts, flushing to database");
+		ourLog.debug("Done saving concepts, flushing to database");
 
 		myConceptDao.flush();
 		myConceptParentChildLinkDao.flush();
 
-		ourLog.info("Done deleting old code system versions");
-
 		if (myDeferredStorageSvc.isStorageQueueEmpty() == false) {
 			ourLog.info("Note that some concept saving has been deferred");
 		}
@@ -612,7 +610,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			return;
 		}
 
-		if (theConceptsStack.size() == 1 || theConceptsStack.size() % 10000 == 0) {
+		if ((theConceptsStack.size() + 1) % 10000 == 0) {
 			float pct = (float) theConceptsStack.size() / (float) theTotalConcepts;
 			ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java

@@ -89,6 +89,33 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 
 	}
 
+
+	@Test
+	public void testValidateQuestionnaireResponseWithValueSetIncludingCompleteCodeSystem() throws IOException {
+		CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/dstu3/iar/CodeSystem-iar-citizenship-status.xml");
+		myCodeSystemDao.create(cs);
+
+		ValueSet vs = loadResourceFromClasspath(ValueSet.class, "/dstu3/iar/ValueSet-iar-citizenship-status.xml");
+		myValueSetDao.create(vs);
+
+		ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+
+//		Questionnaire q = loadResourceFromClasspath(Questionnaire.class,"/dstu3/iar/Questionnaire-iar-test.xml" );
+//		myQuestionnaireDao.create(q);
+//
+//
+//
+//		Bundle bundleForValidation = loadResourceFromClasspath(Bundle.class, "/dstu3/iar/Bundle-for-validation.xml");
+//		try {
+//			MethodOutcome outcome = myBundleDao.validate(bundleForValidation, null, null, null, null, null, null);
+//			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome()));
+//		} catch (PreconditionFailedException e) {
+//			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
+//		}
+	}
+
+
 	@After
 	public void after() {
 		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java

@@ -4,17 +4,21 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
 import ca.uhn.fhir.jpa.config.TestR4WithLuceneDisabledConfig;
 import ca.uhn.fhir.jpa.dao.*;
+import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
+import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
@@ -31,11 +35,13 @@ import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.annotation.Transactional;
 
 import javax.persistence.EntityManager;
-
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.List;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import static org.mockito.ArgumentMatchers.any;
+import static org.junit.Assert.fail;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(classes = {TestR4WithLuceneDisabledConfig.class})
@@ -71,7 +77,7 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 	private IFhirResourceDao<CodeSystem> myCodeSystemDao;
 	@Autowired
 	@Qualifier("myValueSetDaoR4")
-	private IFhirResourceDao<ValueSet> myValueSetDao;
+	private IFhirResourceDaoValueSet<ValueSet, ?, ?> myValueSetDao;
 	@Autowired
 	@Qualifier("myObservationDaoR4")
 	private IFhirResourceDao<Observation> myObservationDao;
@@ -219,6 +225,34 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 
 	}
 
+	protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
+		InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
+		if (stream == null) {
+			fail("Unable to load resource: " + resourceName);
+		}
+		String string = IOUtils.toString(stream, StandardCharsets.UTF_8);
+		IParser newJsonParser = EncodingEnum.detectEncodingNoDefault(string).newParser(myFhirCtx);
+		return newJsonParser.parseResource(type, string);
+	}
+
+
+	/**
+	 * A valueset that includes a whole system (i.e. no properties) should expand
+	 */
+	@Test
+	public void testExpandValueSetContainingSystemIncludeWithNoCodes() throws IOException {
+		CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/dstu3/iar/CodeSystem-iar-citizenship-status.xml");
+		myCodeSystemDao.create(cs);
+
+		ValueSet vs = loadResourceFromClasspath(ValueSet.class, "/dstu3/iar/ValueSet-iar-citizenship-status.xml");
+		myValueSetDao.create(vs);
+
+		ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
+
+		assertEquals(4, expansion.getExpansion().getContains().size());
+
+	}
 
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -730,6 +730,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		assertEquals("The questionnaire \"Questionnaire/DOES_NOT_EXIST\" could not be resolved, so no validation can be performed against the base questionnaire", oo.getIssueFirstRep().getDiagnostics());
 	}
 
+
+
 	private IBaseResource findResourceByIdInBundle(Bundle vss, String name) {
 		IBaseResource retVal = null;
 		for (BundleEntryComponent next : vss.getEntry()) {

hapi-fhir-jpaserver-base/src/test/resources/dstu3/iar/CodeSystem-iar-citizenship-status.xml

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CodeSystem xmlns="http://hl7.org/fhir">
+	<id value="iar-citizenship-status"/>
+	<url value="http://ccim.on.ca/fhir/iar/CodeSystem/iar-citizenship-status"/>
+	<version value="0.1"/>
+	<name value="Citizenship Status"/>
+	<status value="draft"/>
+	<date value="2019-08-22"/>
+	<publisher value="CCIM"/>
+	<contact>
+		<telecom>
+			<system value="other"/>
+			<value value="https://www.ccim.on.ca"/>
+		</telecom>
+	</contact>
+	<compositional value="false"/>
+	<content value="complete"/>
+	<concept>
+		<code value="CDN"/>
+		<display value="Canadian Citizen"/>
+	</concept>
+	<concept>
+		<code value="PR"/>
+		<display value="Permanent Resident"/>
+	</concept>
+	<concept>
+		<code value="TR"/>
+		<display value="Temporary Resident "/>
+	</concept>
+	<concept>
+		<code value="REF"/>
+		<display value="Refugee"/>
+	</concept>
+</CodeSystem>

hapi-fhir-jpaserver-base/src/test/resources/dstu3/iar/ValueSet-iar-citizenship-status.xml

@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ValueSet xmlns="http://hl7.org/fhir">
+	<id value="iar-citizenship-status"/>
+	<url value="http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status"/>
+	<version value="0.1"/>
+	<name value="Citizenship Status"/>
+	<status value="draft"/>
+	<date value="2019-08-08"/>
+	<publisher value="CCIM"/>
+	<contact>
+		<telecom>
+			<system value="other"/>
+			<value value="https://www.ccim.on.ca"/>
+		</telecom>
+	</contact>
+	<compose>
+		<include>
+			<system value="http://ccim.on.ca/fhir/iar/CodeSystem/iar-citizenship-status"/>
+			<version value="0.1"/>
+		</include>
+		<include>
+			<system value="http://hl7.org/fhir/v3/NullFlavor"/>
+			<concept>
+				<code value="UNK"/>
+				<display value="unknown"/>
+			</concept>
+		</include>
+		<include>
+			<system value="http://hl7.org/fhir/v3/NullFlavor"/>
+			<concept>
+				<code value="ASKU"/>
+				<display value="asked but unknown"/>
+			</concept>
+		</include>
+	</compose>
+</ValueSet>

src/changes/changes.xml

@@ -480,6 +480,11 @@
 				JPA servers accidentally stripped the type attribute from the server-exported CapabilityStatement
 				when search parameters of type "special" were found. This has been corrected.
 			</action>
+			<action type="fix">
+				When running the JPA server without Lucene indexing enabled and performing ValueSet expansion,
+				the server would incorrectly ignore inclusion rules that specified a system but no codes (i.e.
+				include the whole system). This has been corrected.
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">