Implement patch in mongo db (#3781)

* Not the final version

* Support PATCH operation

* minor modifications

* minor modifications

* Final version

* Final version

* Version Bump

* bump version again

Co-authored-by: Ken Stevens <ken@smilecdr.com>
This commit is contained in:
Qingyixia 2022-07-17 21:26:34 -04:00 committed by GitHub
parent 8ed0a18ef4
commit 592190701c
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
85 changed files with 120 additions and 121 deletions

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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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-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-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-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -1,8 +1,8 @@
package ca.uhn.fhir.cli;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportJobParameters;
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportJobParameters;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
@ -27,7 +27,6 @@ import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -26,7 +26,17 @@ import ca.uhn.fhir.rest.api.PreferHandlingEnum;
import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.interceptor.*;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc;
import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.SearchPreferHandlingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.StaticCapabilityStatementInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.r4.model.CapabilityStatement;

View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -26,9 +26,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
@ -38,18 +36,13 @@ import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IIdType;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.springframework.batch.core.JobParametersBuilder;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
@ -59,7 +52,6 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import javax.transaction.Transactional;
import java.util.Date;
import java.util.Map;
import java.util.Optional;
import static org.slf4j.LoggerFactory.getLogger;

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@ -134,7 +134,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;

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@ -24,8 +24,6 @@ import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
@ -34,8 +32,6 @@ import org.springframework.data.repository.query.Param;
import java.util.List;
import java.util.Set;
import java.util.Set;
public interface IBatch2JobInstanceRepository extends JpaRepository<Batch2JobInstanceEntity, String>, IHapiFhirJpaRepository {
@Modifying

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@ -22,7 +22,19 @@ package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import javax.persistence.*;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.Version;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;

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@ -20,10 +20,10 @@ package ca.uhn.fhir.jpa.packages;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;

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@ -40,23 +40,19 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import javax.annotation.Nullable;
import javax.servlet.http.HttpServletRequest;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

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@ -25,7 +25,6 @@ import org.apache.lucene.analysis.core.LowerCaseFilterFactory;
import org.apache.lucene.analysis.core.StopFilterFactory;
import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
import org.apache.lucene.analysis.miscellaneous.ASCIIFoldingFilterFactory;
import org.apache.lucene.analysis.miscellaneous.WordDelimiterFilterFactory;
import org.apache.lucene.analysis.miscellaneous.WordDelimiterGraphFilterFactory;
import org.apache.lucene.analysis.ngram.EdgeNGramFilterFactory;
import org.apache.lucene.analysis.ngram.NGramFilterFactory;

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@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;

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@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.dao.predicate.SearchFuzzUtil;

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@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
@ -28,6 +27,7 @@ import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -38,7 +38,6 @@ import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.search.builder.QueryStack;

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@ -17,8 +17,6 @@ import org.mockito.ArgumentCaptor;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageImpl;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
@ -28,7 +26,6 @@ import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;

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@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -30,10 +30,9 @@ import org.hamcrest.Matchers;
import org.springframework.beans.factory.annotation.Autowired;
import java.time.Duration;
import java.util.concurrent.TimeUnit;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.TimeUnit;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.equalTo;

View File

@ -20,10 +20,10 @@ import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.batch2.model.JobWorkNotificationJsonMessage;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.subscription.channel.api.ChannelConsumerSettings;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelFactory;
import ca.uhn.fhir.jpa.subscription.channel.impl.LinkedBlockingChannel;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.jpa.test.Batch2JobHelper;
import ca.uhn.fhir.model.api.IModelJson;

View File

@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.bulk.imprt2;
import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportAppCtx;
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportFileServlet;
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportJobParameters;
@ -13,9 +13,9 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelReceiver;
import ca.uhn.fhir.jpa.subscription.channel.impl.LinkedBlockingChannel;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.test.utilities.ProxyUtil;
import ca.uhn.fhir.test.utilities.server.HttpServletExtension;

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@ -9,9 +9,9 @@ import org.slf4j.LoggerFactory;
import java.math.BigDecimal;
import java.math.MathContext;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.hamcrest.MatcherAssert.assertThat;
public class SearchFuzzUtilTest {
private static final Logger ourLog = LoggerFactory.getLogger(SearchFuzzUtilTest.class);

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@ -25,7 +25,9 @@ import javax.annotation.Nullable;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.*;
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;
public class FhirPatchApplyR4Test {

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@ -4,7 +4,6 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
@ -12,13 +11,11 @@ import org.apache.http.client.methods.HttpPatch;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Media;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.OperationOutcome;
@ -35,7 +32,6 @@ import java.nio.charset.StandardCharsets;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;

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@ -33,7 +33,6 @@ import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.param.UriParam;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;

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@ -1,16 +1,25 @@
package ca.uhn.fhir.jpa.subscription.resthook;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.test.util.StoppableSubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.subscription.BaseSubscriptionsR5Test;
import ca.uhn.fhir.jpa.test.util.StoppableSubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.HapiExtensions;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.SubscriptionTopic;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
@ -19,7 +28,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -24,11 +24,8 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.bulk.export.model;
*/
import com.fasterxml.jackson.annotation.JsonFormat;
import org.springframework.batch.core.BatchStatus;
/**
* This may be in a "jpa" package, but it is not a jpa model!

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-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-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

View File

@ -6,7 +6,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-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-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
</dependency>
</dependencies>
</plugin>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE15-SNAPSHOT</version>
<version>6.1.0-PRE16-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>