Merge branch 'rel_6_4' into nd-4123-bulk-export-stuck-in-finalize-state
This commit is contained in:
nathaniel.doef
commit
1e8a7977b5
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@ -42,7 +42,7 @@ FhirContext ctx = FhirContext.forDstu2();
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ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
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// Encode the output, including the narrative
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String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
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String output = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
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System.out.println(output);
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//END SNIPPET: example1
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@ -21,6 +21,7 @@ package ca.uhn.hapi.fhir.docs;
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*/
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.narrative.CustomThymeleafNarrativeGenerator;
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@SuppressWarnings("unused")
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@ -33,7 +34,11 @@ FhirContext ctx = FhirContext.forDstu2();
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String propFile = "classpath:/com/foo/customnarrative.properties";
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CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator(propFile);
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Patient patient = new Patient();
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ctx.setNarrativeGenerator(gen);
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String output = ctx.newJsonParser().encodeResourceToString(patient);
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System.out.println(output);
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//END SNIPPET: gen
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 4090
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title: "Previously, mdm links that connected resources and golden resources that were newly created had a link score of null,
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this changes it to 1.0 as the golden resource should be a perfect match with the source resource it was created from."
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 4520
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jira: SMILE-4406
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title: "Updating documentation related to narrative generation."
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@ -2,7 +2,7 @@
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HAPI provides several ways to add [Narrative Text](http://hl7.org/fhir/narrative.html) to your encoded messages.
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The simplest way is to simply place the narrative text directly in the resource via the `setDivAsString()` method.
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The simplest way is to place the narrative text directly in the resource via the `setDivAsString()` method.
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```java
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{{snippet:classpath:/ca/uhn/hapi/fhir/docs/Narrative.java|simple}}
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@ -18,7 +18,7 @@ HAPI's built-in narrative generation uses the [Thymeleaf](http://www.thymeleaf.o
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## A Simple Example
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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).
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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)).
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```java
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{{snippet:classpath:/ca/uhn/hapi/fhir/docs/Narrative.java|example1}}
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@ -79,13 +79,16 @@ vitalsigns.profile=http://hl7.org/fhir/StructureDefinition/vitalsigns
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vitalsigns.narrative=classpath:com/example/narrative/Observation_Vitals.html
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```
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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.
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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).
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```properties
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# You can create a template based on a type name
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quantity.dataType=Quantity
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quantity.narrative=classpath:com/example/narrative/Quantity.html
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string.dataType=String
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string.narrative=classpath:com/example/narrative/String.html
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# Or by class name, which can be useful for custom datatypes and structures
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custom_extension.class=com.example.model.MyCustomExtension
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custom_extension.narrative=classpath:com/example/narrative/CustomExtension.html
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@ -105,13 +108,13 @@ Thymeleaf has a concept called Fragments, which allow reusable template portions
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{{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment.properties}}
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```
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The following template declares a fragment (this is `narrative-with-fragment-child.html` in the example above):
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The following template declares `Fragment1` and `Fragment2` as part of file `narrative-with-fragment-child.html`:
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```html
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{{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment-child.html}}
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```
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And the following template uses it (this is `narrative-with-fragment-child.html` in the example above):
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And the following parent template (`narrative-with-fragment-parent.html`) imports `Fragment1` with parameter 'blah':
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```html
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{{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment-parent.html}}
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@ -569,6 +569,10 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
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assertFields(MdmLink::getEidMatch, theExpectedValues);
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}
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protected void assertLinksMatchScore(Double... theExpectedValues) {
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assertFields(MdmLink::getScore, theExpectedValues);
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}
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public SearchParameterMap buildGoldenResourceSearchParameterMap() {
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SearchParameterMap spMap = new SearchParameterMap();
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spMap.setLoadSynchronous(true);
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@ -77,9 +77,12 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
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JpaPid sourcePatient2Pid = runInTransaction(()->myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), sourcePatient2));
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MdmLink possibleDuplicateMdmLink = (MdmLink) myMdmLinkDaoSvc.newMdmLink();
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possibleDuplicateMdmLink.setGoldenResourcePersistenceId(sourcePatient1Pid);
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possibleDuplicateMdmLink.setSourcePersistenceId(sourcePatient2Pid);
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possibleDuplicateMdmLink.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE).setLinkSource(MdmLinkSourceEnum.AUTO);
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possibleDuplicateMdmLink.setGoldenResourcePersistenceId(sourcePatient1Pid)
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.setSourcePersistenceId(sourcePatient2Pid)
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.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE)
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.setLinkSource(MdmLinkSourceEnum.AUTO)
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.setScore(1.0)
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.setRuleCount(1L);
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saveLink(possibleDuplicateMdmLink);
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}
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@ -90,7 +93,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
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List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
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assertThat(list, hasSize(1));
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List<Parameters.ParametersParameterComponent> part = list.get(0).getPart();
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assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
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assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", "1");
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}
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@Test
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@ -100,7 +103,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
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List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
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assertThat("All resources with Patient type found", list, hasSize(3));
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List<Parameters.ParametersParameterComponent> part = list.get(0).getPart();
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assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
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assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", "1");
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}
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@ -68,6 +68,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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assertLinksMatchResult(MATCH);
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assertLinksCreatedNewResource(true);
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assertLinksMatchedByEid(false);
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assertLinksMatchScore(1.0);
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}
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@Test
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@ -79,6 +80,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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assertLinksMatchResult(MATCH);
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assertLinksCreatedNewResource(true);
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assertLinksMatchedByEid(false);
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assertLinksMatchScore(1.0);
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}
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@Test
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@ -93,6 +95,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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assertLinksMatchResult(MATCH, MATCH);
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assertLinksCreatedNewResource(true, true);
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assertLinksMatchedByEid(false, false);
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assertLinksMatchScore(1.0, 1.0);
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}
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@Test
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@ -107,6 +110,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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assertLinksMatchResult(MATCH, MATCH);
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assertLinksCreatedNewResource(true, false);
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assertLinksMatchedByEid(false, false);
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assertLinksMatchScore(1.0, 2.0/3.0);
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}
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@Test
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@ -29,7 +29,7 @@ public final class MdmMatchOutcome {
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public static final MdmMatchOutcome POSSIBLE_DUPLICATE = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_DUPLICATE);
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public static final MdmMatchOutcome NO_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.NO_MATCH);
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public static final MdmMatchOutcome NEW_GOLDEN_RESOURCE_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.MATCH).setCreatedNewResource(true);
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public static final MdmMatchOutcome NEW_GOLDEN_RESOURCE_MATCH = new MdmMatchOutcome(null, 1.0).setMatchResultEnum(MdmMatchResultEnum.MATCH).setCreatedNewResource(true);
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public static final MdmMatchOutcome EID_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.MATCH).setEidMatch(true);
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public static final MdmMatchOutcome POSSIBLE_MATCH = new MdmMatchOutcome(null, null).setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_MATCH);
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@ -145,7 +145,10 @@ public final class MdmMatchOutcome {
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* Returns the normalized score
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*/
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public Double getNormalizedScore() {
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if (myMdmRuleCount == 0) {
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if (myCreatedNewResource) {
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// If we created a new golden resource from this match, the match score must be 1.00
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return 1.0;
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} else if (myMdmRuleCount == 0) {
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return 0.0;
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}
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return score / myMdmRuleCount;
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@ -1,5 +1,25 @@
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package ca.uhn.fhir.batch2.jobs.export;
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/*-
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* #%L
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* hapi-fhir-storage-batch2-jobs
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* %%
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* Copyright (C) 2014 - 2023 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.batch2.model.StatusEnum;
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import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
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import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
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@ -4,6 +4,7 @@ bundle.resourceType = Bundle
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bundle.style = thymeleaf
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bundle.narrative = classpath:ca/uhn/fhir/narrative/narrative-with-fragment-parent.html
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# Fragment template
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fragment1.fragmentName = MyFragment
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fragment1.style = thymeleaf
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fragment1.narrative = classpath:ca/uhn/fhir/narrative/narrative-with-fragment-child.html
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