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Remote Terminology support refactor (#3822) 

* Revert "test passes with a lot of copy/paste"

This reverts commit f2f28e22ef.

* make translateOutcomeToResults public

* double RAM

* final consolidation.  move shared code out to static utility methods

* revert azure memory
disable jacoco on jpaserver test prokect

* bump hapi version

* rebump hapi to PRE-21

* licenses

Co-authored-by: Ken Stevens <ken@smilecdr.com>
This commit is contained in:
Ken Stevens 2022-07-25 11:47:31 -04:00 committed by GitHub
parent 611c1d9d2c
commit f01e4a7ad2
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
70 changed files with 199 additions and 192 deletions
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2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-batch/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-bom/pom.xml
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@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,7 @@
<parent>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
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<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
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@ -4,7 +4,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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2
hapi-fhir-docs/pom.xml
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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jacoco/pom.xml
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@ -11,7 +11,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
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@ -5,7 +5,7 @@
<parent>
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2
hapi-fhir-jpaserver-base/pom.xml
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@ -5,7 +5,7 @@
<parent>
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2
hapi-fhir-jpaserver-cql/pom.xml
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@ -7,7 +7,7 @@
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2
hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
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@ -6,7 +6,7 @@
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2
hapi-fhir-jpaserver-mdm/pom.xml
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@ -6,7 +6,7 @@
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2
hapi-fhir-jpaserver-model/pom.xml
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@ -5,7 +5,7 @@
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2
hapi-fhir-jpaserver-searchparam/pom.xml
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@ -5,7 +5,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/BaseSubscriptionDeliverySubscriber.java
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@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.subscription.match.deliver;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.HookParams;
@ -29,7 +28,6 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryMessage;
import com.google.common.annotations.VisibleForTesting;
import org.slf4j.Logger;

1
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionRegisteringSubscriber.java
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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.subscription.match.matcher.subscriber;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;

2
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/match/deliver/BaseSubscriptionDeliverySubscriberTest.java
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@ -46,9 +46,7 @@ import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.fail;

2
hapi-fhir-jpaserver-test-utilities/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu3Test.java
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@ -6,9 +6,9 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
import ca.uhn.fhir.jpa.subscription.NotificationServlet;
import ca.uhn.fhir.jpa.test.util.SubscriptionTestUtil;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.test.util.SubscriptionTestUtil;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
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<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-server-mdm/pom.xml
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@ -7,7 +7,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2
hapi-fhir-server-openapi/pom.xml
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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server/pom.xml
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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
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@ -5,7 +5,7 @@
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<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
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@ -5,7 +5,7 @@
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2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
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@ -5,7 +5,7 @@
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2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
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2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
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@ -5,7 +5,7 @@
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2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
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@ -5,7 +5,7 @@
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2
hapi-fhir-spring-boot/pom.xml
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@ -5,7 +5,7 @@
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2
hapi-fhir-sql-migrate/pom.xml
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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage-batch2-jobs/pom.xml
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@ -5,7 +5,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2
hapi-fhir-storage-batch2/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage-mdm/pom.xml
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@ -5,7 +5,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage-test-utilities/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage/pom.xml
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@ -5,7 +5,7 @@
<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

1
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionCanonicalizer.java
View File

@ -53,7 +53,6 @@ import javax.annotation.Nullable;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.stream.Collectors;
import static ca.uhn.fhir.util.HapiExtensions.EX_SEND_DELETE_MESSAGES;

2
hapi-fhir-structures-dstu2.1/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-testpage-overlay/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu3/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r4/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r5/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

115
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupport.java
View File

@ -1,15 +1,10 @@
package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.TranslateConceptResult;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.i18n.Msg;
@ -18,12 +13,9 @@ import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import org.slf4j.Logger;
@ -32,8 +24,6 @@ import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -345,7 +335,7 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
IGenericClient client = provideClient();
FhirContext fhirContext = client.getFhirContext();
IBaseParameters params = buildTranslateInputParameters(fhirContext, theRequest);
IBaseParameters params = RemoteTerminologyUtil.buildTranslateInputParameters(fhirContext, theRequest);
IBaseParameters outcome = client
.operation()
@ -354,7 +344,7 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
.withParameters(params)
.execute();
return translateOutcomeToResults(fhirContext, outcome);
return RemoteTerminologyUtil.translateOutcomeToResults(fhirContext, outcome);
}
private IGenericClient provideClient() {
@ -443,7 +433,6 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
return params;
}
/**
* Sets the FHIR Terminology Server base URL
*
@ -467,104 +456,4 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
Validate.notNull(theClientInterceptor, "theClientInterceptor must not be null");
myClientInterceptors.add(theClientInterceptor);
}
private IBaseParameters buildTranslateInputParameters(FhirContext fhirContext, TranslateCodeRequest theRequest) {
IBaseParameters params = ParametersUtil.newInstance(fhirContext);
if (!StringUtils.isEmpty(theRequest.getConceptMapUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "url", theRequest.getConceptMapUrl());
}
if (!StringUtils.isEmpty(theRequest.getConceptMapVersion())) {
ParametersUtil.addParameterToParametersString(fhirContext, params, "conceptMapVersion", theRequest.getConceptMapVersion());
}
if (theRequest.getCodings() != null) {
addCodingsToTranslateParameters(fhirContext, theRequest.getCodings(), params);
}
if (!StringUtils.isEmpty(theRequest.getSourceValueSetUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "source", theRequest.getSourceValueSetUrl());
}
if (!StringUtils.isEmpty(theRequest.getTargetValueSetUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "target", theRequest.getTargetValueSetUrl());
}
if (!StringUtils.isEmpty(theRequest.getTargetSystemUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "targetsystem", theRequest.getTargetSystemUrl());
}
if (theRequest.isReverse()) {
ParametersUtil.addParameterToParametersBoolean(fhirContext, params, "reverse", theRequest.isReverse());
}
return params;
}
private void addCodingsToTranslateParameters(FhirContext fhirContext, List<IBaseCoding> theCodings, IBaseParameters theParams) {
BaseRuntimeElementCompositeDefinition<?> codeableConceptDef = (BaseRuntimeElementCompositeDefinition<?>) Objects.requireNonNull(fhirContext.getElementDefinition("CodeableConcept"));
BaseRuntimeChildDefinition codings = codeableConceptDef.getChildByName("coding");
BaseRuntimeElementCompositeDefinition<?> codingDef = (BaseRuntimeElementCompositeDefinition<?>) Objects.requireNonNull(fhirContext.getElementDefinition("Coding"));
BaseRuntimeChildDefinition codingSystemChild = codingDef.getChildByName("system");
BaseRuntimeChildDefinition codingCodeChild = codingDef.getChildByName("code");
BaseRuntimeElementDefinition<IPrimitiveType<?>> systemDef = (RuntimePrimitiveDatatypeDefinition) fhirContext.getElementDefinition("uri");
BaseRuntimeElementDefinition<IPrimitiveType<?>> codeDef = (RuntimePrimitiveDatatypeDefinition) fhirContext.getElementDefinition("code");
IBase codeableConcept = codeableConceptDef.newInstance();
for (IBaseCoding aCoding : theCodings) {
IBaseCoding newCoding = (IBaseCoding) codingDef.newInstance();
IPrimitiveType<?> newSystem = systemDef.newInstance(aCoding.getSystem());
codingSystemChild.getMutator().addValue(newCoding, newSystem);
IPrimitiveType<?> newCode = codeDef.newInstance(aCoding.getCode());
codingCodeChild.getMutator().addValue(newCoding, newCode);
codings.getMutator().addValue(codeableConcept, newCoding);
}
ParametersUtil.addParameterToParameters(fhirContext, theParams, "codeableConcept", codeableConcept);
}
public TranslateConceptResults translateOutcomeToResults(FhirContext fhirContext, IBaseParameters outcome) {
Optional<String> result = ParametersUtil.getNamedParameterValueAsString(fhirContext, outcome, "result");
Optional<String> message = ParametersUtil.getNamedParameterValueAsString(fhirContext, outcome, "message");
List<IBase> matches = ParametersUtil.getNamedParameters(fhirContext, outcome, "match");
TranslateConceptResults retVal = new TranslateConceptResults();
if (result.isPresent()) {
retVal.setResult(Boolean.parseBoolean(result.get()));
}
if (message.isPresent()) {
retVal.setMessage(message.get());
}
if (!matches.isEmpty()) {
retVal.setResults(matchesToTranslateConceptResults(fhirContext, matches));
}
return retVal;
}
private List<TranslateConceptResult> matchesToTranslateConceptResults(FhirContext fhirContext, List<IBase> theMatches) {
List<TranslateConceptResult> resultList = new ArrayList();
for (IBase m : theMatches) {
TranslateConceptResult match = new TranslateConceptResult();
String equivalence = ParametersUtil.getParameterPartValueAsString(fhirContext, m, "equivalence");
Optional<IBase> concept = ParametersUtil.getParameterPartValue(fhirContext, m, "concept");
String source = ParametersUtil.getParameterPartValueAsString(fhirContext, m, "source");
if (StringUtils.isNotBlank(equivalence)) {
match.setEquivalence(equivalence);
}
if (concept.isPresent()) {
IBaseCoding matchedCoding = (IBaseCoding) concept.get();
match.setSystem(matchedCoding.getSystem());
match.setCode(matchedCoding.getCode());
match.setDisplay(matchedCoding.getDisplay());
if (StringUtils.isNotBlank(source)) {
match.setConceptMapUrl(source);
}
resultList.add(match);
}
}
return resultList;
}
}

124
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyUtil.java Normal file
View File

@ -0,0 +1,124 @@
package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.TranslateConceptResult;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
public final class RemoteTerminologyUtil {
private RemoteTerminologyUtil() {}
public static IBaseParameters buildTranslateInputParameters(FhirContext fhirContext, IValidationSupport.TranslateCodeRequest theRequest) {
IBaseParameters params = ParametersUtil.newInstance(fhirContext);
if (!StringUtils.isEmpty(theRequest.getConceptMapUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "url", theRequest.getConceptMapUrl());
}
if (!StringUtils.isEmpty(theRequest.getConceptMapVersion())) {
ParametersUtil.addParameterToParametersString(fhirContext, params, "conceptMapVersion", theRequest.getConceptMapVersion());
}
if (theRequest.getCodings() != null) {
addCodingsToTranslateParameters(fhirContext, theRequest.getCodings(), params);
}
if (!StringUtils.isEmpty(theRequest.getSourceValueSetUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "source", theRequest.getSourceValueSetUrl());
}
if (!StringUtils.isEmpty(theRequest.getTargetValueSetUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "target", theRequest.getTargetValueSetUrl());
}
if (!StringUtils.isEmpty(theRequest.getTargetSystemUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "targetsystem", theRequest.getTargetSystemUrl());
}
if (theRequest.isReverse()) {
ParametersUtil.addParameterToParametersBoolean(fhirContext, params, "reverse", theRequest.isReverse());
}
return params;
}
public static void addCodingsToTranslateParameters(FhirContext fhirContext, List<IBaseCoding> theCodings, IBaseParameters theParams) {
BaseRuntimeElementCompositeDefinition<?> codeableConceptDef = (BaseRuntimeElementCompositeDefinition<?>) Objects.requireNonNull(fhirContext.getElementDefinition("CodeableConcept"));
BaseRuntimeChildDefinition codings = codeableConceptDef.getChildByName("coding");
BaseRuntimeElementCompositeDefinition<?> codingDef = (BaseRuntimeElementCompositeDefinition<?>) Objects.requireNonNull(fhirContext.getElementDefinition("Coding"));
BaseRuntimeChildDefinition codingSystemChild = codingDef.getChildByName("system");
BaseRuntimeChildDefinition codingCodeChild = codingDef.getChildByName("code");
BaseRuntimeElementDefinition<IPrimitiveType<?>> systemDef = (RuntimePrimitiveDatatypeDefinition) fhirContext.getElementDefinition("uri");
BaseRuntimeElementDefinition<IPrimitiveType<?>> codeDef = (RuntimePrimitiveDatatypeDefinition) fhirContext.getElementDefinition("code");
IBase codeableConcept = codeableConceptDef.newInstance();
for (IBaseCoding aCoding : theCodings) {
IBaseCoding newCoding = (IBaseCoding) codingDef.newInstance();
IPrimitiveType<?> newSystem = systemDef.newInstance(aCoding.getSystem());
codingSystemChild.getMutator().addValue(newCoding, newSystem);
IPrimitiveType<?> newCode = codeDef.newInstance(aCoding.getCode());
codingCodeChild.getMutator().addValue(newCoding, newCode);
codings.getMutator().addValue(codeableConcept, newCoding);
}
ParametersUtil.addParameterToParameters(fhirContext, theParams, "codeableConcept", codeableConcept);
}
public static TranslateConceptResults translateOutcomeToResults(FhirContext fhirContext, IBaseParameters outcome) {
Optional<String> result = ParametersUtil.getNamedParameterValueAsString(fhirContext, outcome, "result");
Optional<String> message = ParametersUtil.getNamedParameterValueAsString(fhirContext, outcome, "message");
List<IBase> matches = ParametersUtil.getNamedParameters(fhirContext, outcome, "match");
TranslateConceptResults retVal = new TranslateConceptResults();
if (result.isPresent()) {
retVal.setResult(Boolean.parseBoolean(result.get()));
}
if (message.isPresent()) {
retVal.setMessage(message.get());
}
if (!matches.isEmpty()) {
retVal.setResults(matchesToTranslateConceptResults(fhirContext, matches));
}
return retVal;
}
private static List<TranslateConceptResult> matchesToTranslateConceptResults(FhirContext fhirContext, List<IBase> theMatches) {
List<TranslateConceptResult> resultList = new ArrayList();
for (IBase m : theMatches) {
TranslateConceptResult match = new TranslateConceptResult();
String equivalence = ParametersUtil.getParameterPartValueAsString(fhirContext, m, "equivalence");
Optional<IBase> concept = ParametersUtil.getParameterPartValue(fhirContext, m, "concept");
String source = ParametersUtil.getParameterPartValueAsString(fhirContext, m, "source");
if (StringUtils.isNotBlank(equivalence)) {
match.setEquivalence(equivalence);
}
if (concept.isPresent()) {
IBaseCoding matchedCoding = (IBaseCoding) concept.get();
match.setSystem(matchedCoding.getSystem());
match.setCode(matchedCoding.getCode());
match.setDisplay(matchedCoding.getDisplay());
if (StringUtils.isNotBlank(source)) {
match.setConceptMapUrl(source);
}
resultList.add(match);
}
}
return resultList;
}
}

16
hapi-tinder-plugin/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -58,37 +58,37 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>

2
hapi-tinder-test/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
pom.xml
View File

@ -6,7 +6,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description>
<url>https://hapifhir.io</url>
@ -2015,7 +2015,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-checkstyle</artifactId>
<!-- Remember to bump this when you upgrade the version -->
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
</dependency>
</dependencies>
</plugin>

2
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE20-SNAPSHOT</version>
<version>6.1.0-PRE21-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>