Fixing parser for contained resources

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);
@@ -1238,7 +1238,8 @@ 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);
 							nextRef.setResource(target);
@@ -1285,7 +1286,7 @@ public void wereBack() {
 			super.wereBack();
 
 			IResource nextResource = (IResource) getCurrentElement();
-			String version = ResourceMetadataKeyEnum.VERSION.get(nextResource);
+			String version = nextResource.getId().getVersionIdPart();
 			String resourceName = myContext.getResourceType(nextResource);
 			String bundleIdPart = nextResource.getId().getIdPart();
 			if (isNotBlank(bundleIdPart)) {

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

@@ -118,6 +118,9 @@
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;
 import jakarta.persistence.EntityManager;
+
+import java.util.Objects;
+
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -195,6 +198,7 @@
 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;
@@ -562,6 +566,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	@Autowired
 	protected IJobCoordinator myJobCoordinator;
 
+	private IValidationPolicyAdvisor policyAdvisor;
 	@RegisterExtension
 	private final PreventDanglingInterceptorsExtension myPreventDanglingInterceptorsExtension = new PreventDanglingInterceptorsExtension(()-> myInterceptorRegistry);
 
@@ -1076,8 +1081,12 @@ public ReferenceValidationPolicy policyForReference(IResourceValidator validator
 
 		@Override
 		public IValidationPolicyAdvisor getPolicyAdvisor() {
-			return this;
-		}
+		  if (Objects.isNull(policyAdvisor)) {
+			  return new BasePolicyAdvisorForFullValidation(getReferencePolicy());
+		  }
+
+		  return policyAdvisor;
+	  }
 
 		@Override
 		public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -585,7 +585,7 @@ 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
@@ -1324,11 +1324,11 @@ public void testEncodeContainedResources() {
 		// Adding medication to Contained.
 		Medication medResource = new Medication();
 		medResource.setCode(codeDt);
-		medResource.setId("#" + medId);
+		medResource.setId(medId);
 		medicationPrescript.getContained().add(medResource);
 
 		// Medication reference. This should point to the contained resource.
-		Reference medRefDt = new Reference("#" + medId);
+		Reference medRefDt = new Reference(medId);
 		medRefDt.setDisplay("MedRef");
 		medicationPrescript.setMedication(medRefDt);
 
@@ -1339,7 +1339,7 @@ public void testEncodeContainedResources() {
 		// @formatter:on
 		assertThat(encoded).
 			contains("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
-				"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
+				"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"123\"/>",
 				"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>");
 
 	}
@@ -1836,45 +1836,6 @@ public void testEncodeNarrativeSuppressed() {
 		assertThat(encoded).contains("maritalStatus");
 	}
 
-	@Test
-	public void testEncodeNonContained() {
-		// Create an organization
-		Organization org = new Organization();
-		org.setId("Organization/65546");
-		org.getNameElement().setValue("Contained Test Organization");
-
-		// Create a patient
-		Patient patient = new Patient();
-		patient.setId("Patient/1333");
-		patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
-		patient.getManagingOrganization().setResource(org);
-
-		// Create a list containing both resources. In a server method, you might just
-		// return this list, but here we will create a bundle to encode.
-		List<IBaseResource> resources = new ArrayList<IBaseResource>();
-		resources.add(org);
-		resources.add(patient);
-
-		// Create a bundle with both
-		Bundle b = new Bundle();
-		b.addEntry().setResource(org);
-		b.addEntry().setResource(patient);
-
-		// Encode the buntdle
-		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
-		ourLog.info(encoded);
-		assertThat(encoded).doesNotContain("<contained>");
-		assertThat(encoded).contains("<Organization", "<id value=\"65546\"/>", "</Organization>");
-		assertThat(encoded).contains("<reference value=\"Organization/65546\"/>");
-		assertThat(encoded).contains("<Patient", "<id value=\"1333\"/>", "</Patient>");
-
-		encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(encoded);
-		assertThat(encoded).doesNotContain("<contained>");
-		assertThat(encoded).contains("<reference value=\"Organization/65546\"/>");
-
-	}
-
 	/**
 	 * See #312
 	 */
@@ -2055,17 +2016,17 @@ public void testEncodeWithContained() {
 
 		// Will be added by reference
 		Patient p = new Patient();
-		p.setId("#" + "1000");
+		p.setId("1000");
 		contained.add(p);
 
 		// Will be added by direct resource object
 		Location l = new Location();
-		l.setId("#" + "1001");
+		l.setId("1001");
 		contained.add(l);
 
 		// Will not be referred to (and therefore shouldn't appear in output)
 		Location l2 = new Location();
-		l2.setId("#1002");
+		l2.setId("1002");
 		contained.add(l2);
 
 		Appointment appointment = new Appointment();
@@ -3084,7 +3045,7 @@ public void testParseContainedBinaryResource() {
 
 		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(manifest);
 		ourLog.info(encoded);
-		assertThat(encoded).contains("contained>", "<Binary", "</contained>");
+		assertThat(encoded).contains("<contained>", "<Binary", "</contained>");
 
 		DocumentManifest actual = ourCtx.newXmlParser().parseResource(DocumentManifest.class, encoded);
 		assertThat(actual.getContained()).hasSize(1);
@@ -3410,10 +3371,10 @@ public void testParseWovenContainedResources() throws IOException {
 
 		DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
 		Observation obs = (Observation) resource.getResult().get(1).getResource();
-		assertEquals("#2", obs.getId());
+		assertEquals("2", obs.getId());
 		Reference performerFirstRep = obs.getPerformerFirstRep();
 		Practitioner performer = (Practitioner) performerFirstRep.getResource();
-		assertEquals("#3", performer.getId());
+		assertEquals("3", performer.getId());
 	}
 
 	/**

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/HapiWorkerContext.java

@@ -40,6 +40,7 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -413,8 +414,14 @@ public StructureDefinition fetchTypeDefinition(String theTypeName) {
 	}
 
 	@Override
-	public List<StructureDefinition> fetchTypeDefinitions(String s) {
-		return List.of(fetchTypeDefinition(s));
+	public List<StructureDefinition> fetchTypeDefinitions(String input) {
+		List<StructureDefinition> types = new ArrayList<>();
+		for (StructureDefinition sd : allStructures()) {
+			if (input.equals(sd.getTypeTail())) {
+				types.add(sd);
+			}
+		}
+		return types;
 	}
 
 	@Override
@@ -461,7 +468,11 @@ public <T extends org.hl7.fhir.r4.model.Resource> T fetchResourceWithException(C
 
 	@Override
 	public <T extends Resource> List<T> fetchResourcesByType(Class<T> aClass) {
-		return List.of();
+		List<T> res = new ArrayList<>();
+		if (aClass == StructureDefinition.class) {
+			res.addAll((Collection<? extends T>) getStructures());
+		}
+		return res;
 	}
 
 	@Override

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/narrative/CustomThymeleafNarrativeGeneratorR4Test.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.narrative;
 
 import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.r4.model.Meta;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.StringType;
@@ -49,6 +50,7 @@ public void testCustomType() {
 		myCtx.setNarrativeGenerator(null);
 
 		CustomPatient patient = new CustomPatient();
+		patient.setMeta(new Meta().addProfile("http://custom_patient"));
 		patient.setActive(true);
 		FavouritePizzaExtension parentExtension = new FavouritePizzaExtension();
 		parentExtension.setToppings(new StringType("Mushrooms, Onions"));

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

@@ -1093,7 +1093,7 @@ public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocal
 		Observation obs = new Observation();
 
 		Patient pt = new Patient();
-		pt.setId("#1");
+		pt.setId("1");
 		pt.addName().setFamily("FAM");
 		obs.getSubject().setReference("#1");
 		obs.getContained().add(pt);
@@ -1106,8 +1106,8 @@ public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocal
 		ourLog.info(encoded);
 
 		obs = ourCtx.newJsonParser().parseResource(Observation.class, encoded);
-		assertEquals("#1", obs.getContained().get(0).getId());
-		assertEquals(enc.getId(), obs.getContained().get(1).getId());
+		assertEquals("1", obs.getContained().get(0).getId());
+		assertEquals(enc.getId(), "#" + obs.getContained().get(1).getId());
 
 		pt = (Patient) obs.getSubject().getResource();
 		assertEquals("FAM", pt.getNameFirstRep().getFamily());
@@ -1126,7 +1126,7 @@ public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocal
 		obs.getSubject().setResource(pt);
 
 		Encounter enc = new Encounter();
-		enc.setId("#1");
+		enc.setId("1");
 		enc.setStatus(Encounter.EncounterStatus.ARRIVED);
 		obs.getEncounter().setReference("#1");
 		obs.getContained().add(enc);
@@ -1135,8 +1135,8 @@ public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocal
 		ourLog.info(encoded);
 
 		obs = ourCtx.newJsonParser().parseResource(Observation.class, encoded);
-		assertEquals("#1", obs.getContained().get(0).getId());
-		assertEquals(pt.getId(), obs.getContained().get(1).getId());
+		assertEquals("1", obs.getContained().get(0).getId());
+		assertEquals(pt.getId(), "#" + obs.getContained().get(1).getId());
 
 		pt = (Patient) obs.getSubject().getResource();
 		assertEquals("FAM", pt.getNameFirstRep().getFamily());
@@ -1162,8 +1162,8 @@ public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocal
 		ourLog.info(encoded);
 		mr = ourCtx.newJsonParser().parseResource(MedicationRequest.class, encoded);
 
-		assertEquals(pract.getId(), mr.getContained().get(0).getId());
-		assertEquals(med.getId(), mr.getContained().get(1).getId());
+		assertEquals(pract.getId(), "#" + mr.getContained().get(0).getId());
+		assertEquals(med.getId(), "#" + mr.getContained().get(1).getId());
 
 	}
 
@@ -1675,8 +1675,8 @@ public void testParseAndEncodePreservesContainedResourceOrder() {
 
 		ourLog.info("Input: {}", auditEvent);
 		AuditEvent ae = ourCtx.newJsonParser().parseResource(AuditEvent.class, auditEvent);
-		assertEquals("#A", ae.getContained().get(0).getId());
-		assertEquals("#B", ae.getContained().get(1).getId());
+		assertEquals("A", ae.getContained().get(0).getId());
+		assertEquals("B", ae.getContained().get(1).getId());
 		assertEquals("#B", ae.getEntity().get(0).getWhat().getReference());
 		assertEquals("#A", ae.getEntity().get(1).getWhat().getReference());
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java

@@ -114,8 +114,8 @@ public void testParseAndEncodePreservesContainedResourceOrder() {
 
 		ourLog.info("Input: {}", auditEvent);
 		AuditEvent ae = ourCtx.newXmlParser().parseResource(AuditEvent.class, auditEvent);
-		assertEquals("#A", ae.getContained().get(0).getId());
-		assertEquals("#B", ae.getContained().get(1).getId());
+		assertEquals("A", ae.getContained().get(0).getId());
+		assertEquals("B", ae.getContained().get(1).getId());
 		assertEquals("#B", ae.getEntity().get(0).getWhat().getReference());
 		assertEquals("#A", ae.getEntity().get(1).getWhat().getReference());