Merge branch 'rel_6_4' into nd-4123-bulk-export-stuck-in-finalize-state

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/Narrative.java

@@ -42,7 +42,7 @@ FhirContext ctx = FhirContext.forDstu2();
 ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 
 // Encode the output, including the narrative
-String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
+String output = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
 System.out.println(output);
 //END SNIPPET: example1
 

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/NarrativeGenerator.java

@@ -21,6 +21,7 @@ package ca.uhn.hapi.fhir.docs;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.narrative.CustomThymeleafNarrativeGenerator;
 
 @SuppressWarnings("unused")
@@ -33,7 +34,11 @@ FhirContext ctx = FhirContext.forDstu2();
 String propFile = "classpath:/com/foo/customnarrative.properties";
 CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator(propFile);
 
+Patient patient = new Patient();
+
 ctx.setNarrativeGenerator(gen);
+String output = ctx.newJsonParser().encodeResourceToString(patient);
+System.out.println(output);
 //END SNIPPET: gen
 
 	

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4090-mdm-score-null-for-links-with-new-golden-resource.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4090
+title: "Previously, mdm links that connected resources and golden resources that were newly created had a link score of null,
+this changes it to 1.0 as the golden resource should be a perfect match with the source resource it was created from."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/450-update-to-narrative-generation-documentation.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4520
+jira: SMILE-4406
+title: "Updating documentation related to narrative generation."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/model/narrative_generation.md

@@ -2,7 +2,7 @@
 
 HAPI provides several ways to add [Narrative Text](http://hl7.org/fhir/narrative.html) to your encoded messages.
 
-The simplest way is to simply place the narrative text directly in the resource via the `setDivAsString()` method.
+The simplest way is to place the narrative text directly in the resource via the `setDivAsString()` method.
 
 ```java
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/Narrative.java|simple}}
@@ -18,7 +18,7 @@ HAPI's built-in narrative generation uses the [Thymeleaf](http://www.thymeleaf.o
 
 ## A Simple Example
 
-Activating HAPI's built-in narrative generator is as simple as calling [setNarrativeGenerator](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/context/FhirContext.html#setNarrativeGenerator(ca.uhn.fhir.narrative.INarrativeGenerator).
+Activating HAPI's built-in narrative generator is as simple as calling [setNarrativeGenerator](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/context/FhirContext.html#setNarrativeGenerator(ca.uhn.fhir.narrative.INarrativeGenerator)).
 
 ```java
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/Narrative.java|example1}}
@@ -79,13 +79,16 @@ vitalsigns.profile=http://hl7.org/fhir/StructureDefinition/vitalsigns
 vitalsigns.narrative=classpath:com/example/narrative/Observation_Vitals.html
 ```
 
-You may also override/define behaviour for datatypes and other structures. These datatype narrative definitions will be used as content within <code>th:narrative</code> blocks in resource templates. See the example resource template above for an example.
+You may also override/define behaviour for datatypes and other structures. These datatype narrative definitions will be used as content within <code>th:narrative</code> blocks in resource templates. See the [example above](#creating-your-own-templates).
 
 ```properties
 # You can create a template based on a type name
 quantity.dataType=Quantity
 quantity.narrative=classpath:com/example/narrative/Quantity.html
 
+string.dataType=String
+string.narrative=classpath:com/example/narrative/String.html
+
 # Or by class name, which can be useful for custom datatypes and structures
 custom_extension.class=com.example.model.MyCustomExtension
 custom_extension.narrative=classpath:com/example/narrative/CustomExtension.html
@@ -105,13 +108,13 @@ Thymeleaf has a concept called Fragments, which allow reusable template portions
 {{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment.properties}}
 ```
 
-The following template declares a fragment (this is `narrative-with-fragment-child.html` in the example above):
+The following template declares `Fragment1` and `Fragment2` as part of file `narrative-with-fragment-child.html`: 
 
 ```html
 {{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment-child.html}}
 ```
 
-And the following template uses it (this is `narrative-with-fragment-child.html` in the example above):
+And the following parent template (`narrative-with-fragment-parent.html`) imports `Fragment1` with parameter 'blah':
 
 ```html
 {{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment-parent.html}}

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java

@@ -569,6 +569,10 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
 		assertFields(MdmLink::getEidMatch, theExpectedValues);
 	}
 
+	protected void assertLinksMatchScore(Double... theExpectedValues) {
+		assertFields(MdmLink::getScore, theExpectedValues);
+	}
+
 	public SearchParameterMap buildGoldenResourceSearchParameterMap() {
 		SearchParameterMap spMap = new SearchParameterMap();
 		spMap.setLoadSynchronous(true);

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderQueryLinkR4Test.java

@@ -77,9 +77,12 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		JpaPid sourcePatient2Pid = runInTransaction(()->myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), sourcePatient2));
 
 		MdmLink possibleDuplicateMdmLink = (MdmLink) myMdmLinkDaoSvc.newMdmLink();
-		possibleDuplicateMdmLink.setGoldenResourcePersistenceId(sourcePatient1Pid);
+		possibleDuplicateMdmLink.setGoldenResourcePersistenceId(sourcePatient1Pid)
-		possibleDuplicateMdmLink.setSourcePersistenceId(sourcePatient2Pid);
+			.setSourcePersistenceId(sourcePatient2Pid)
-		possibleDuplicateMdmLink.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE).setLinkSource(MdmLinkSourceEnum.AUTO);
+			.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE)
+			.setLinkSource(MdmLinkSourceEnum.AUTO)
+			.setScore(1.0)
+			.setRuleCount(1L);
 		saveLink(possibleDuplicateMdmLink);
 	}
 
@@ -90,7 +93,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
 		assertThat(list, hasSize(1));
 		List<Parameters.ParametersParameterComponent> part = list.get(0).getPart();
-		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
+		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", "1");
 	}
 
 	@Test
@@ -100,7 +103,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
 		assertThat("All resources with Patient type found", list, hasSize(3));
 		List<Parameters.ParametersParameterComponent> part = list.get(0).getPart();
-		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
+		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", "1");
 	}
 
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java

@@ -68,6 +68,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH);
 		assertLinksCreatedNewResource(true);
 		assertLinksMatchedByEid(false);
+		assertLinksMatchScore(1.0);
 	}
 
 	@Test
@@ -79,6 +80,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH);
 		assertLinksCreatedNewResource(true);
 		assertLinksMatchedByEid(false);
+		assertLinksMatchScore(1.0);
 	}
 
 	@Test
@@ -93,6 +95,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH, MATCH);
 		assertLinksCreatedNewResource(true, true);
 		assertLinksMatchedByEid(false, false);
+		assertLinksMatchScore(1.0, 1.0);
 	}
 
 	@Test
@@ -107,6 +110,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH, MATCH);
 		assertLinksCreatedNewResource(true, false);
 		assertLinksMatchedByEid(false, false);
+		assertLinksMatchScore(1.0, 2.0/3.0);
 	}
 
 	@Test

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/MdmMatchOutcome.java

@@ -29,7 +29,7 @@ public final class MdmMatchOutcome {
 
 	public static final MdmMatchOutcome POSSIBLE_DUPLICATE = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_DUPLICATE);
 	public static final MdmMatchOutcome NO_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.NO_MATCH);
-	public static final MdmMatchOutcome NEW_GOLDEN_RESOURCE_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.MATCH).setCreatedNewResource(true);
+	public static final MdmMatchOutcome NEW_GOLDEN_RESOURCE_MATCH = new MdmMatchOutcome(null, 1.0).setMatchResultEnum(MdmMatchResultEnum.MATCH).setCreatedNewResource(true);
 	public static final MdmMatchOutcome EID_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.MATCH).setEidMatch(true);
 	public static final MdmMatchOutcome POSSIBLE_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_MATCH);
 
@@ -145,7 +145,10 @@ public final class MdmMatchOutcome {
 	 * 	Returns the normalized score
 	 */
 	public Double getNormalizedScore() {
-		if (myMdmRuleCount == 0) {
+		if (myCreatedNewResource) {
+			// If we created a new golden resource from this match, the match score must be 1.00
+			return 1.0;
+		} else if (myMdmRuleCount == 0) {
 			return 0.0;
 		}
 		return score / myMdmRuleCount;

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/BulkExportUtil.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.batch2.jobs.export;
 
+/*-
+ * #%L
+ * hapi-fhir-storage-batch2-jobs
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import ca.uhn.fhir.batch2.model.StatusEnum;
 import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
 import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;

hapi-fhir-test-utilities/src/main/resources/ca/uhn/fhir/narrative/narrative-with-fragment.properties

@@ -4,6 +4,7 @@ bundle.resourceType        = Bundle
 bundle.style               = thymeleaf
 bundle.narrative           = classpath:ca/uhn/fhir/narrative/narrative-with-fragment-parent.html
 
+# Fragment template
 fragment1.fragmentName     = MyFragment
 fragment1.style            = thymeleaf
 fragment1.narrative        = classpath:ca/uhn/fhir/narrative/narrative-with-fragment-child.html