Bump org.hl7.fhir.core to 6.4.4

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java

@@ -399,7 +399,7 @@ public void wereBack() {
 				myErrorHandler.containedResourceWithNoId(null);
 			} else {
 				if (!res.getId().isLocal()) {
-					res.setId(new IdDt('#' + res.getId().getIdPart()));
+					res.setId(new IdDt(res.getId().getIdPart()));
 				}
 				getPreResourceState().getContainedResources().put(res.getId().getValueAsString(), res);
 			}
@@ -439,7 +439,7 @@ public void wereBack() {
 				// need an ID to be referred to)
 				myErrorHandler.containedResourceWithNoId(null);
 			} else {
-				res.getIdElement().setValue('#' + res.getIdElement().getIdPart());
+				res.getIdElement().setValue(res.getIdElement().getIdPart());
 				getPreResourceState()
 						.getContainedResources()
 						.put(res.getIdElement().getValue(), res);
@@ -1238,12 +1238,13 @@ void weaveContainedResources() {
 				String ref = nextRef.getReferenceElement().getValue();
 				if (isNotBlank(ref)) {
 					if (ref.startsWith("#") && ref.length() > 1) {
-						IBaseResource target = myContainedResources.get(ref);
+						String refId = ref.substring(1);
+						IBaseResource target = myContainedResources.get(refId);
 						if (target != null) {
-							ourLog.debug("Resource contains local ref {}", ref);
+							ourLog.debug("Resource contains local ref {}", refId);
 							nextRef.setResource(target);
 						} else {
-							myErrorHandler.unknownReference(null, ref);
+							myErrorHandler.unknownReference(null, refId);
 						}
 					}
 				}

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

@@ -38,6 +38,7 @@
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import com.google.common.collect.Lists;
@@ -1507,16 +1508,7 @@ public ContainedResources containResources(IBaseResource theResource, OptionsEnu
 		ContainedResources contained = new ContainedResources();
 
 		List<? extends IBaseResource> containedResources = getContainedResourceList(theResource);
-		for (IBaseResource next : containedResources) {
-			String nextId = next.getIdElement().getValue();
-			if (StringUtils.isNotBlank(nextId)) {
-				if (!nextId.startsWith("#")) {
-					nextId = '#' + nextId;
-				}
-				next.getIdElement().setValue(nextId);
-			}
-			contained.addContained(next);
-		}
+		containedResources.forEach(contained::addContained);
 
 		if (myContext.getParserOptions().isAutoContainReferenceTargetsWithNoId()) {
 			containResourcesForEncoding(contained, theResource, modifyResource);
@@ -1809,10 +1801,12 @@ public IIdType addContained(IBaseResource theResource) {
 			if (existing != null) {
 				return existing;
 			}
-
-			IIdType newId = theResource.getIdElement();
+			
+			IIdType newId = new IdDt(theResource.getIdElement());
 			if (isBlank(newId.getValue())) {
-				newId.setValue("#" + UUID.randomUUID());
+				UUID randomUUID = UUID.randomUUID();
+				theResource.getIdElement().setValue(randomUUID.toString());
+				newId.setValue("#" + randomUUID);
 			}
 
 			getResourceToIdMap().put(theResource, newId);

hapi-fhir-jpaserver-hfql/src/test/java/ca/uhn/fhir/jpa/fql/executor/HfqlExecutorTest.java

@@ -198,7 +198,7 @@ select foo()
 		IHfqlExecutionResult result = myHfqlExecutor.executeInitialSearch(statement, null, mySrd);
 		IHfqlExecutionResult.Row row = result.getNextRow();
 		assertEquals(IHfqlExecutionResult.ROW_OFFSET_ERROR, row.getRowOffset());
-		assertEquals("Failed to evaluate FHIRPath expression \"foo()\". Error: HAPI-2404: Error in ?? at 1, 1: The name foo is not a valid function name", row.getRowValues().get(0));
+		assertEquals("Failed to evaluate FHIRPath expression \"foo()\". Error: HAPI-2404: Error @1, 1: The name foo is not a valid function name", row.getRowValues().get(0));
 		assertFalse(result.hasNext());
 	}
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java

@@ -208,5 +208,10 @@ public boolean conformsToProfile(FHIRPathEngine engine, Object appContext, Base
 		public ValueSet resolveValueSet(FHIRPathEngine engine, Object appContext, String url) {
 			return null;
 		}
+
+		@Override
+		public boolean paramIsType(String name, int index) {
+			return false;
+		}
 	}
 }

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java

@@ -462,11 +462,18 @@ private void extractSearchIndexParametersForTargetResources(
 
 	private IBaseResource findContainedResource(Collection<IBaseResource> resources, IBaseReference reference) {
 		for (IBaseResource resource : resources) {
-			if (resource.getIdElement().equals(reference.getReferenceElement())) return resource;
+			String idElementId = resource.getIdElement().getValueAsString();
+			String referenceElementId = reference.getReferenceElement().getValueAsString();
+			if (containedResourceEquals(idElementId, referenceElementId)) return resource;
 		}
 		return null;
 	}
 
+	private static boolean containedResourceEquals(String idElementId, String referenceElementId) {
+		String normalizedIdElementId = idElementId.startsWith("#") ? idElementId : "#" + idElementId;
+		return StringUtils.equals(normalizedIdElementId, referenceElementId);
+	}
+
 	private void mergeParams(ResourceIndexedSearchParams theSrcParams, ResourceIndexedSearchParams theTargetParams) {
 
 		theTargetParams.myNumberParams.addAll(theSrcParams.myNumberParams);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/ChainingR4SearchTest.java

@@ -715,7 +715,7 @@ public void testShouldResolveAThreeLinkChainWithAContainedResourceAtTheEndOfTheC
 			obs.getCode().addCoding().setCode("obs2").setSystem("Some System").setDisplay("Body weight as measured by me");
 			obs.setStatus(Observation.ObservationStatus.FINAL);
 			obs.setValue(new Quantity(81));
-			obs.setSubject(new Reference(p.getId()));
+			obs.setSubject(new Reference("#" + p.getId()));
 			obs.setEncounter(new Reference(encounter.getId()));
 			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 

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

@@ -1518,7 +1518,7 @@ public void testSearchParameterDescendsIntoContainedResource() {
 		mySearchParamRegistry.forceRefresh();
 
 		Specimen specimen = new Specimen();
-		specimen.setId("#FOO");
+		specimen.setId("FOO");
 		specimen.setReceivedTimeElement(new DateTimeType("2011-01-01"));
 		Observation o = new Observation();
 		o.setId("O1");
@@ -1529,7 +1529,7 @@ public void testSearchParameterDescendsIntoContainedResource() {
 		myObservationDao.update(o);
 
 		specimen = new Specimen();
-		specimen.setId("#FOO");
+		specimen.setId("FOO");
 		specimen.setReceivedTimeElement(new DateTimeType("2011-01-03"));
 		o = new Observation();
 		o.setId("O2");

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java

@@ -3224,7 +3224,7 @@ public void testTransactionWithContainedResource() {
 		patient = myPatientDao.read(new IdType(id));
 
 		assertThat(patient.getManagingOrganization().getReference()).containsPattern(HASH_UUID_PATTERN);
-		assertEquals(patient.getManagingOrganization().getReference(), patient.getContained().get(0).getId());
+		assertEquals(patient.getManagingOrganization().getReference(), "#" + patient.getContained().get(0).getId());
 	}
 
 	@Nonnull

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java

@@ -193,6 +193,7 @@
 import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.validation.instance.advisor.BasePolicyAdvisorForFullValidation;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Order;
@@ -1069,6 +1070,18 @@ public boolean isSuppressMessageId(String path, String messageId) {
 		public ReferenceValidationPolicy getReferencePolicy() {
 			return ReferenceValidationPolicy.IGNORE;
 		}
+
+		@Override
+		public IValidationPolicyAdvisor getPolicyAdvisor() {
+			return new BasePolicyAdvisorForFullValidation(getReferencePolicy());
+		}
+
+		@Override
+		public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {
+			return null;
+		}
+
+
 	}
 
 

hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/config/MdmRuleValidatorTest.java

@@ -76,7 +76,7 @@ public void testMatcherBadFhirPath() throws IOException {
 		try {
 			setMdmRuleJson("bad-rules-bad-fhirpath.json");
 			fail();		} catch (ConfigurationException e) {
-			assertThat(e.getMessage()).startsWith(Msg.code(1518) + "MatchField [given-name] resourceType [Patient] has failed FHIRPath evaluation.  Error in ?? at 1, 1: The name blurst is not a valid function name");
+			assertThat(e.getMessage()).startsWith(Msg.code(1518) + "MatchField [given-name] resourceType [Patient] has failed FHIRPath evaluation.  Error @1, 1: The name blurst is not a valid function name");
 		}
 	}
 

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorPolicyAdvisor.java

@@ -31,6 +31,7 @@
 import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.validation.instance.advisor.BasePolicyAdvisorForFullValidation;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -123,6 +124,16 @@ public boolean isSuppressMessageId(String path, String messageId) {
 		return false;
 	}
 
+	@Override
+	public IValidationPolicyAdvisor getPolicyAdvisor() {
+		return new BasePolicyAdvisorForFullValidation(getReferencePolicy());
+	}
+
+	@Override
+	public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {
+		return null;
+	}
+
 	@Override
 	public ReferenceValidationPolicy getReferencePolicy() {
 		return ReferenceValidationPolicy.IGNORE;

hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcherTest.java

@@ -15,6 +15,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.utils.XVerExtensionManager;
+import org.hl7.fhir.r5.utils.validation.ValidatorSession;
 import org.hl7.fhir.validation.instance.InstanceValidator;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -56,7 +57,7 @@ public void checkFetchByUrl() {
     InstanceValidator v = new InstanceValidator(
       wrappedWorkerContext,
       new FhirInstanceValidator.NullEvaluationContext(),
-      new XVerExtensionManager(null));
+      new XVerExtensionManager(null), new ValidatorSession());
     RequestDetails r = new SystemRequestDetails();
     // test
     Element returnedResource = fetcher.fetch(v, r,"http://www.test-url-for-questionnaire.com/Questionnaire/test-id|1.0.0");

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2_1Test.java

@@ -403,7 +403,7 @@ public void testEncodeAndParseContained() {
 
 		assertNotNull(patient.getManagingOrganization().getResource());
 		org = (Organization) patient.getManagingOrganization().getResource();
-		assertEquals("#" + organizationUuid, org.getIdElement().getValue());
+		assertEquals(organizationUuid, org.getIdElement().getValue());
 		assertEquals("Contained Test Organization", org.getName());
 
 		// And re-encode a second time

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/CustomTypeDstu2Test.java

@@ -80,7 +80,7 @@ public void testConstrainedFieldContainedResource() {
 
 		medication = (Medication) mo.getMedication().getResource();
 		assertNotNull(medication);
-		assertEquals("#" + medicationUuid, medication.getId().getValue());
+		assertEquals(medicationUuid, medication.getId().getValue());
 		assertEquals("MED TEXT", medication.getCode().getText());
 
 	}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -76,6 +76,7 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.UUID;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -1391,7 +1392,7 @@ public void testParseAndEncodeBundle() throws Exception {
 	 */
 	@Test
 	public void testParseAndEncodeBundleFromXmlToJson() throws Exception {
-		String content = IOUtils.toString(JsonParserDstu2Test.class.getResourceAsStream("/bundle-example2.xml"));
+		String content = IOUtils.toString(Objects.requireNonNull(JsonParserDstu2Test.class.getResourceAsStream("/bundle-example2.xml")), StandardCharsets.UTF_8);
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, content);
 
@@ -1400,7 +1401,7 @@ public void testParseAndEncodeBundleFromXmlToJson() throws Exception {
 
 		Medication m = (Medication) ((ResourceReferenceDt) p.getMedication()).getResource();
 		assertNotNull(m);
-		assertEquals("#med", m.getId().getValue());
+		assertEquals("med", m.getId().getValue());
 		assertThat(p.getContained().getContainedResources()).hasSize(1);
 		assertThat(p.getContained().getContainedResources().get(0)).isSameAs(m);
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -90,6 +90,7 @@
 import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Objects;
 import java.util.UUID;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -221,18 +222,18 @@ public void testParseXmlModifierExtensionWithoutUrl() {
 	 */
 	@Test
 	public void testParseWovenContainedResources() throws IOException {
-		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
+		String string = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("/bundle_with_woven_obs.xml")), StandardCharsets.UTF_8);
 
 		IParser parser = ourCtx.newXmlParser();
 		parser.setParserErrorHandler(new StrictErrorHandler());
 		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = parser.parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, string);
 
 		DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
 		Observation obs = (Observation) resource.getResult().get(1).getResource();
-		assertEquals("#2", obs.getId().getValue());
+		assertEquals("2", obs.getId().getValue());
 		ResourceReferenceDt performerFirstRep = obs.getPerformer().get(0);
 		Practitioner performer = (Practitioner) performerFirstRep.getResource();
-		assertEquals("#3", performer.getId().getValue());
+		assertEquals("3", performer.getId().getValue());
 	}
 
 	@Test
@@ -301,13 +302,13 @@ public void testContainedResourceWithNoIdLenient() throws IOException {
 	@Test
 	public void testParseWithInvalidLocalRef() throws IOException {
 		try {
-			String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
+			String string = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml")), StandardCharsets.UTF_8);
 
 			IParser parser = ourCtx.newXmlParser();
 			parser.setParserErrorHandler(new StrictErrorHandler());
 			parser.parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, string);
 			fail();		} catch (DataFormatException e) {
-			assertEquals(Msg.code(1851) + "DataFormatException at [[row,col {unknown-source}]: [47,7]]: " + Msg.code(1826) + "Resource has invalid reference: #1", e.getMessage());
+			assertEquals(Msg.code(1851) + "DataFormatException at [[row,col {unknown-source}]: [47,7]]: " + Msg.code(1826) + "Resource has invalid reference: 1", e.getMessage());
 		}
 	}
 
@@ -536,7 +537,7 @@ public void testEncodeAndParseContained() {
 
 		assertNotNull(patient.getManagingOrganization().getResource());
 		org = (Organization) patient.getManagingOrganization().getResource();
-		assertEquals("#" + organizationUuid, org.getId().getValue());
+		assertEquals(organizationUuid, org.getId().getValue());
 		assertEquals("Contained Test Organization", org.getName());
 
 		// And re-encode a second time
@@ -568,6 +569,35 @@ public void testEncodeAndParseContained() {
 
 	}
 
+	@Test
+	void testEncodeContainedResourceWithNoExplicitId() {
+		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		String organizationUuid = UUID.randomUUID().toString();
+		// Create an organization, note that the organization does not have an ID
+		Organization org = new Organization();
+		org.getNameElement().setValue("Contained Test Organization");
+		org.setId(organizationUuid);
+
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
+
+		// Put the organization as a reference in the patient resource
+		patient.getManagingOrganization().setResource(org);
+
+
+		//patient.getContained().getContainedResources().clear();
+		patient.getManagingOrganization().setReference((String) null);
+		String encoded = xmlParser.encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded).containsSubsequence(Arrays.asList("<contained>", "<Organization ", "<id value=\"" + organizationUuid +
+			"\"/>", "</Organization", "</contained>", "<reference value=\"#" + organizationUuid + "\"/>"));
+		assertThat(encoded).doesNotContainPattern("(?s)<contained>.*<Org.*<contained>");
+		assertThat(encoded).contains("<reference value=\"#" + organizationUuid + "\"/>");
+
+	}
+
 	@Test
 	public void testEncodeAndParseContainedCustomTypes() {
 		ourCtx = FhirContext.forDstu2();
@@ -2953,11 +2983,7 @@ public static void afterClassClearContext() {
 		TestUtil.randomizeLocaleAndTimezone();
 	}
 
-	public static void main(String[] args) {
-		IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
-		// c.registerInterceptor(new LoggingInterceptor(true));
-		c.read().resource("Patient").withId("324").execute();
-	}
+
 
 	public static void compareXml(String content, String reEncoded) {
 		Diff d = DiffBuilder.compare(Input.fromString(content))