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 hashLessId = ref.substring(1);
+						IBaseResource target = myContainedResources.get(hashLessId);
 						if (target != null) {
-							ourLog.debug("Resource contains local ref {}", ref);
+							ourLog.debug("Resource contains local ref {}", hashLessId);
 							nextRef.setResource(target);
 						} else {
-							myErrorHandler.unknownReference(null, ref);
+							myErrorHandler.unknownReference(null, hashLessId);
 						}
 					}
 				}

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;
@@ -1428,6 +1429,18 @@ public boolean acceptUndeclaredExtension(
 		});
 	}
 
+	private boolean isInternalFragment(IBaseReference theReference) {
+		assert theReference.getResource() != null;
+		if (theReference.getResource().getIdElement().isEmpty()) {
+			return true;
+		}
+		if (theReference.getResource().getIdElement().isAbsolute()
+				|| theReference.getResource().getIdElement().getValueAsString().startsWith("urn:")) {
+			return false;
+		}
+		return true;
+	}
+
 	private void containResourcesForEncoding(
 			ContainedResources theContained, IBaseResource theResource, boolean theModifyResource) {
 		List<IBaseReference> allReferences = getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
@@ -1456,17 +1469,17 @@ private void containResourcesForEncoding(
 		for (IBaseReference next : allReferences) {
 			IBaseResource resource = next.getResource();
 			if (resource != null) {
-				if (resource.getIdElement().isEmpty() || resource.getIdElement().isLocal()) {
+				if (resource.getIdElement().isEmpty() || isInternalFragment(next)) {
 
 					IIdType id = theContained.addContained(resource);
 					if (id == null) {
 						continue;
 					}
 					if (theModifyResource) {
 						getContainedResourceList(theResource).add(resource);
-						next.setReference(id.getValue());
+						next.setReference("#" + id.getValue());
 					}
-					if (resource.getIdElement().isLocal() && theContained.hasExistingIdToContainedResource()) {
+					if (isInternalFragment(next) && theContained.hasExistingIdToContainedResource()) {
 						theContained
 								.getExistingIdToContainedResource()
 								.remove(resource.getIdElement().getValue());
@@ -1508,13 +1521,6 @@ public ContainedResources containResources(IBaseResource theResource, OptionsEnu
 
 		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);
 		}
 
@@ -1810,14 +1816,20 @@ public IIdType addContained(IBaseResource theResource) {
 				return existing;
 			}
 
-			IIdType newId = theResource.getIdElement();
+			final 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);
+				// TODO put newId in resourceToIdMap ?
+				getResourceToIdMap().put(theResource, newId);
+			} else {
+				// TODO put new IdDt with # in resourceToIdMap ?
+				getResourceToIdMap().put(theResource, new IdDt("#" + newId.getIdPart()));
 			}
-
-			getResourceToIdMap().put(theResource, newId);
+			// getResourceToIdMap().put(theResource, newId);
 			getOrCreateResourceList().add(theResource);
-			return newId;
+			return theResource.getIdElement();
 		}
 
 		public void addContained(IIdType theId, IBaseResource theResource) {

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/BaseSearchParamExtractor.java

@@ -50,6 +50,7 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.model.primitive.BoundCodeDt;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.param.DateParam;
@@ -2237,7 +2238,7 @@ private void extractResourceLinkFromReference(
 				IBaseReference valueRef) {
 			IIdType nextId = valueRef.getReferenceElement();
 			if (nextId.isEmpty() && valueRef.getResource() != null) {
-				nextId = valueRef.getResource().getIdElement();
+				nextId = new IdDt("#" + valueRef.getResource().getIdElement());
 			}
 
 			if (nextId == null || nextId.isEmpty()) {

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

@@ -462,7 +462,8 @@ private void extractSearchIndexParametersForTargetResources(
 
 	private IBaseResource findContainedResource(Collection<IBaseResource> resources, IBaseReference reference) {
 		for (IBaseResource resource : resources) {
-			if (resource.getIdElement().equals(reference.getReferenceElement())) return resource;
+			if (("#" + resource.getIdElement())
+					.equals(reference.getReferenceElement().toString())) return resource;
 		}
 		return null;
 	}

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

@@ -77,7 +77,7 @@ public void validation_Jpa_Bundle_MeasureReferencesLibraryAndLibrary() {
 
 		final ValidationResult validationResult = validator.validateWithResult(bundleWithBadLibrary);
 
-		assertEquals(12, validationResult.getMessages().stream().filter(errorMessagePredicate()).count());
+		assertEquals(10, validationResult.getMessages().stream().filter(errorMessagePredicate()).count());
 	}
 
 	@Test
@@ -94,7 +94,7 @@ public void validation_Jpa_Bundle_MeasureOnly() {
 
 		final ValidationResult validationResult = validator.validateWithResult(bundleWithMeasureOnly );
 
-		assertEquals(10, validationResult.getMessages().stream().filter(errorMessagePredicate()).count());
+		assertEquals(8, validationResult.getMessages().stream().filter(errorMessagePredicate()).count());
 	}
 
 	@Test
@@ -108,7 +108,7 @@ public void validation_Jpa_Bundle_MeasureOnly_NoLibraryReference() {
 
 		final ValidationResult validationResult = validator.validateWithResult(bundleWithMeasureOnlyNoLibraryReference);
 
-		assertEquals(9, validationResult.getMessages().stream().filter(errorMessagePredicate()).count());
+		assertEquals(7, validationResult.getMessages().stream().filter(errorMessagePredicate()).count());
 	}
 
 	@Test

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

@@ -94,7 +94,7 @@ public void testValidateInvalidExpression() {
 			myDao.validateResourceForStorage(nextSearchParameter, null);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(1121) + "Invalid FHIRPath format for SearchParameter.expression \"Patient.ex[[[\": Error in ?? at 1, 1: Found [ expecting a token name", e.getMessage());
+			assertEquals(Msg.code(1121) + "Invalid FHIRPath format for SearchParameter.expression \"Patient.ex[[[\": Error @1, 1: Found [ expecting a token name", e.getMessage());
 		}
 	}
 

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

@@ -715,8 +715,8 @@ 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.setEncounter(new Reference(encounter.getId()));
+			obs.setSubject(new Reference("#" +p.getId()));
+			obs.setEncounter(new Reference("#" + encounter.getId()));
 			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
 			// Create a dummy record so that an unconstrained query doesn't pass the test due to returning the only record
@@ -1025,7 +1025,7 @@ public void testShouldResolveAThreeLinkChainWithQualifiersWithAContainedResource
 			Patient p = new Patient();
 			p.setId("pat");
 			p.addName().setFamily("Smith").addGiven("John");
-			p.getManagingOrganization().setReference(org.getId());
+			p.getManagingOrganization().setReference("#" + org.getId());
 
 			Observation obs = new Observation();
 			obs.getContained().add(p);
@@ -1036,7 +1036,7 @@ public void testShouldResolveAThreeLinkChainWithQualifiersWithAContainedResource
 
 			Device d = new Device();
 			d.setId("dev");
-			d.getOwner().setReference(org.getId());
+			d.getOwner().setReference("#" + org.getId());
 
 			Observation obs2 = new Observation();
 			obs2.getContained().add(d);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -168,7 +168,7 @@ public void testCreateLinkCreatesAppropriatePaths_ContainedResource() {
 		myPatientDao.update(p, mySrd);
 
 		Observation containedObs = new Observation();
-		containedObs.setId("#cont");
+		containedObs.setId("cont");
 		containedObs.setSubject(new Reference("Patient/A"));
 
 		Encounter enc = new Encounter();
@@ -285,7 +285,7 @@ public void testCreateLinkCreatesAppropriatePaths_ContainedResourceRecursive_ToO
 		p.setManagingOrganization(new Reference("Organization/ABC"));
 
 		Observation containedObs = new Observation();
-		containedObs.setId("#cont");
+		containedObs.setId("cont");
 		containedObs.setSubject(new Reference("#pat"));
 
 		Encounter enc = new Encounter();
@@ -754,7 +754,7 @@ public void testTagsInContainedResourcesPreserved() {
 		assertEquals(organizationUuid, organizationUuidParsed);
 
 		Organization org = (Organization) p.getManagingOrganization().getResource();
-		assertEquals("#" + organizationUuid, org.getId());
+		assertEquals(organizationUuid, org.getId());
 		assertThat(org.getMeta().getTag()).hasSize(1);
 
 	}

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

@@ -852,7 +852,7 @@ public void testValidateProfileTargetType_PolicyCheckExistsAndType() throws IOEx
 		obs.setSubject(new Reference("Group/ABC"));
 		oo = validateAndReturnOutcome(obs);
 		ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
-		assertThat(oo.getIssueFirstRep().getDiagnostics()).as(encode(oo)).isEqualTo("Unable to find a match for profile Group/ABC (by type) among choices: ; [CanonicalType[http://hl7.org/fhir/StructureDefinition/Patient]]");
+		assertThat(oo.getIssueFirstRep().getDiagnostics()).as(encode(oo)).isEqualTo("Unable to find a match for profile Group/ABC (by type) among choices: ; [http://hl7.org/fhir/StructureDefinition/Patient]");
 
 		// Target of right type
 		obs.setSubject(new Reference("Patient/DEF"));

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

@@ -195,6 +195,7 @@
 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;
@@ -1073,6 +1074,16 @@ 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;
@@ -127,4 +128,14 @@ 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-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 +57,8 @@ 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
@@ -817,7 +817,7 @@ public void testEncodeBinaryWithNoContentType() {
 	public void testEncodeBundleWithContained() {
 		DiagnosticReport rpt = new DiagnosticReport();
 		rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Sharp1")).setId("#1"));
-		rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Uuid1")).setId("urn:uuid:UUID1"));
+		rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Uuid1")).setId("https//example.org/UUID1"));
 
 		Bundle b = new Bundle();
 		b.addEntry().setResource(rpt);