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Fix "is-a" ValueSet expansion and add "descendent-of" support #5603

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Fix "is-a" ValueSet expansion and add "descendent-of" support #5603

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b265e05
Fix "is-a" ValueSet expansion, add "descendent-of" support
ohetrifork Jan 18, 2024
81c6b84
Merge branch 'hapifhir:master' into master
ohetrifork Jan 18, 2024
f638159
Fixed tests in DSTU3 and R5
ohetrifork Jan 19, 2024
46c672b
Trigger new build
ohetrifork Jan 22, 2024
cc48c4f
Revert "Trigger new build"
ohetrifork Jan 22, 2024
c207b49
fix default partition setting on resource (#5617)
fil512 Jan 22, 2024
29fec70
pom bump, doc add, version enum add (#5616)
longma1 Jan 22, 2024
949c970
fix default partition setting on resource (#5618)
michaelabuckley Jan 22, 2024
51a6dda
Add setting to make broker not use JacksonMessageConverter (#5611)
jmarchionatto Jan 26, 2024
3fc67dc
Merge branch 'hapifhir:master' into master
ohetrifork Jan 30, 2024
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2 changes: 1 addition & 1 deletion hapi-deployable-pom/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-android/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-base/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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4 changes: 3 additions & 1 deletion hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
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Expand Up @@ -134,7 +134,9 @@ public enum VersionEnum {
V6_10_3,
V6_11_0,

V7_0_0;
V7_0_0,
V7_1_0,
V7_2_0;

public static VersionEnum latestVersion() {
VersionEnum[] values = VersionEnum.values();
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4 changes: 2 additions & 2 deletions hapi-fhir-bom/pom.xml
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Expand Up @@ -4,15 +4,15 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>

<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-checkstyle/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-cli/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-client-okhttp/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-client/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-converter/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-dist/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-docs/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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5 changes: 5 additions & 0 deletions ...c/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5617-fix-default-partition-setting.yaml
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@@ -0,0 +1,5 @@
---
type: fix
issue: 5617
title: "Resource UserData RESOURCE_PARTITION_ID was incorrectly being set to null for the default partition.
This has been corrected to use RequestPartitionId.defaultPartition()"
2 changes: 1 addition & 1 deletion hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/version.yaml
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@@ -1,3 +1,3 @@
---
release-date: "2023-02-18"
codename: "TBD"
codename: "Apollo"
5 changes: 5 additions & 0 deletions ...a/uhn/hapi/fhir/changelog/7_2_0/5610-allow-broker-other-than-jacksonmessageconverter.yaml
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---
type: add
issue: 5610
title: "Before, message broker always used `JacksonMessageConverter`. Added a configuration option that allows
to disable it so other converters can be configured depending on the message type."
Empty file added hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/upgrade.md
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3 changes: 3 additions & 0 deletions hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/version.yaml
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@@ -0,0 +1,3 @@
---
release-date: "2023-05-18"
codename: "Borealis"
2 changes: 1 addition & 1 deletion hapi-fhir-jacoco/pom.xml
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Expand Up @@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jaxrsserver-base/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpa/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-base/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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3 changes: 2 additions & 1 deletion hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaStorageResourceParser.java
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Expand Up @@ -23,6 +23,7 @@
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
Expand Down Expand Up @@ -248,7 +249,7 @@ private <R extends IBaseResource> void populateResourcePartitionInformation(
myPartitionLookupSvc.getPartitionById(partitionId.getPartitionId());
retVal.setUserData(Constants.RESOURCE_PARTITION_ID, persistedPartition.toRequestPartitionId());
} else {
retVal.setUserData(Constants.RESOURCE_PARTITION_ID, null);
retVal.setUserData(Constants.RESOURCE_PARTITION_ID, RequestPartitionId.defaultPartition());
}
}
}
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10 changes: 10 additions & 0 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java
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Expand Up @@ -1596,6 +1596,16 @@ private void handleFilterConceptAndCode(
TermConcept code = findCodeForFilterCriteria(theSystem, theFilter);

if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
ourLog.debug(
" * Filtering on specific code and codes with a parent of {}/{}/{}",
code.getId(),
code.getCode(),
code.getDisplay());

b.must(f.bool()
.should(f.match().field("myParentPids").matching("" + code.getId()))
.should(f.match().field("myId").matching(code.getId())));
} else if (theFilter.getOp() == ValueSet.FilterOperator.DESCENDENTOF) {
ourLog.debug(
" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());

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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion ...ties/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
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Expand Up @@ -786,7 +786,7 @@ public void testExpandWithIsAInExternalValueSet() {
logAndValidateValueSet(result);

ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
}

@Test
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-hfql/pom.xml
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Expand Up @@ -3,7 +3,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-ips/pom.xml
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Expand Up @@ -3,7 +3,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-mdm/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-model/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java
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Expand Up @@ -263,7 +263,7 @@ public class JpaConstants {
/**
* The name of the default partition
*/
public static final String DEFAULT_PARTITION_NAME = "DEFAULT";
public static final String DEFAULT_PARTITION_NAME = ProviderConstants.DEFAULT_PARTITION_NAME;

/**
* The name of the collection of all partitions
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-searchparam/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-subscription/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-dstu2/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-dstu3/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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10 changes: 5 additions & 5 deletions ...st-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
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Expand Up @@ -313,7 +313,7 @@ public void testExpandWithCodesAndDisplayFilterBlank() {
.setSystem(codeSystem.getUrl())
.addFilter()
.setProperty("concept")
.setOp(FilterOperator.ISA)
.setOp(FilterOperator.DESCENDENTOF)
.setValue("dogs");

myValueSetDao.create(valueSet, mySrd);
Expand Down Expand Up @@ -504,7 +504,7 @@ public void testExpandWithIsAInExternalValueSet() {
logAndValidateValueSet(result);

ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));

}

Expand Down Expand Up @@ -535,7 +535,7 @@ public void testExpandWithIsAInExternalValueSetReindex() {
logAndValidateValueSet(result);

ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));

}

Expand Down Expand Up @@ -650,7 +650,7 @@ public void testIndexingIsDeferredForLargeCodeSystems() {
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");

ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
Expand All @@ -669,7 +669,7 @@ public void testIndexingIsDeferredForLargeCodeSystems() {
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);

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2 changes: 1 addition & 1 deletion .../test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetVersionedTest.java
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Expand Up @@ -230,7 +230,7 @@ private ValueSet createLocalVs(String theCodeSystemUrl, String theValueSetVersio
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(theCodeSystemUrl);
include.setVersion(theValueSetVersion);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
return myLocalVs;

}
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-r4/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.10-SNAPSHOT</version>
<version>7.1.0-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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