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batch2 management operations api (#3742) 

* first test passes.  onto the next one

* two down two to go

* three down one to go

* licenses

* basic admin-json plumbing confirmed with IT

* FIXME

* FIXME

* FIXME

* FIXME

* changelog

* bump hapi version to 6.1.0-PRE6-SNAPSHOT

Co-authored-by: Ken Stevens <ken@smilecdr.com>
This commit is contained in:
Ken Stevens 2022-06-28 23:02:17 -04:00 committed by GitHub
parent 84fe58cc86
commit 069f20a5f7
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
133 changed files with 1091 additions and 132 deletions
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2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/PagingIterator.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.model.api;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import java.util.Iterator;

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/api/IBatchJobSubmitter.java
View File

@ -25,6 +25,10 @@ import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
/**
* @deprecated we are in the process of converting to batch2
*/
@Deprecated
public interface IBatchJobSubmitter {
/**

4
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/svc/BatchJobSubmitterImpl.java
View File

@ -37,6 +37,10 @@ import org.springframework.transaction.annotation.Transactional;
import static org.slf4j.LoggerFactory.getLogger;
/**
* @deprecated we are in the process of converting to batch2
*/
@Deprecated
public class BatchJobSubmitterImpl implements IBatchJobSubmitter {
private static final Logger ourLog = getLogger(BatchJobSubmitterImpl.class);

4
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-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-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
View File

@ -22,9 +22,9 @@ package ca.uhn.fhir.jpa.demo;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import org.apache.commons.dbcp2.BasicDataSource;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

20
hapi-fhir-client-okhttp/src/main/java/ca/uhn/fhir/okhttp/client/OkHttpRestfulClient.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.okhttp.client;
/*-
* #%L
* HAPI FHIR OkHttp Client
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3742-batch2-api.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: add
issue: 3742
title: "Added operations to batch2 api for searching job instances."

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

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.batch2;
*/
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.batch2.coordinator.BatchWorkChunk;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.StatusEnum;
@ -42,6 +43,7 @@ import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.UUID;
import java.util.function.Consumer;
import java.util.stream.Collectors;
@ -111,6 +113,21 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
return fetchInstance(theInstanceId);
}
public List<JobInstance> fetchInstancesByJobDefinitionIdAndStatus(String theJobDefinitionId, Set<StatusEnum> theRequestedStatuses, int thePageSize, int thePageIndex) {
PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.ASC, "myCreateTime");
return toInstanceList(myJobInstanceRepository.fetchInstancesByJobDefinitionIdAndStatus(theJobDefinitionId, theRequestedStatuses, pageRequest));
}
@Override
public List<JobInstance> fetchInstancesByJobDefinitionId(String theJobDefinitionId, int thePageSize, int thePageIndex) {
PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.ASC, "myCreateTime");
return toInstanceList(myJobInstanceRepository.findInstancesByJobDefinitionId(theJobDefinitionId, pageRequest));
}
private List<JobInstance> toInstanceList(List<Batch2JobInstanceEntity> theInstancesByJobDefinitionId) {
return theInstancesByJobDefinitionId.stream().map(this::toInstance).collect(Collectors.toList());
}
@Override
@Nonnull
public Optional<JobInstance> fetchInstance(String theInstanceId) {
@ -264,7 +281,19 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
}
@Override
public void cancelInstance(String theInstanceId) {
myJobInstanceRepository.updateInstanceCancelled(theInstanceId, true);
public JobOperationResultJson cancelInstance(String theInstanceId) {
int recordsChanged = myJobInstanceRepository.updateInstanceCancelled(theInstanceId, true);
String operationString = "Cancel job instance " + theInstanceId;
if (recordsChanged > 0) {
return JobOperationResultJson.newSuccess(operationString, "Job instance <" + theInstanceId + "> successfully cancelled.");
} else {
Optional<JobInstance> instance = fetchInstance(theInstanceId);
if (instance.isPresent()) {
return JobOperationResultJson.newFailure(operationString, "Job instance <" + theInstanceId + "> was already cancelled. Nothing to do.");
} else {
return JobOperationResultJson.newFailure(operationString, "Job instance <" + theInstanceId + "> not found.");
}
}
}
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ObservationLastNIndexPersistSvc.java
View File

@ -20,7 +20,8 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
@ -31,10 +32,16 @@ import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import ca.uhn.fhir.jpa.searchparam.extractor.PathAndRef;
import ca.uhn.fhir.parser.IParser;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.*;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.UUID;
public class ObservationLastNIndexPersistSvc {

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2JobInstanceRepository.java
View File

@ -22,11 +22,15 @@ package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
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;
import org.springframework.data.repository.query.Param;
import java.util.List;
import java.util.Set;
public interface IBatch2JobInstanceRepository extends JpaRepository<Batch2JobInstanceEntity, String>, IHapiFhirJpaRepository {
@Modifying
@ -35,9 +39,15 @@ public interface IBatch2JobInstanceRepository extends JpaRepository<Batch2JobIns
@Modifying
@Query("UPDATE Batch2JobInstanceEntity e SET e.myCancelled = :cancelled WHERE e.myId = :id")
void updateInstanceCancelled(@Param("id") String theInstanceId, @Param("cancelled") boolean theCancelled);
int updateInstanceCancelled(@Param("id") String theInstanceId, @Param("cancelled") boolean theCancelled);
@Modifying
@Query("UPDATE Batch2JobInstanceEntity e SET e.myCurrentGatedStepId = :currentGatedStepId WHERE e.myId = :id")
void updateInstanceCurrentGatedStepId(@Param("id") String theInstanceId, @Param("currentGatedStepId") String theCurrentGatedStepId);
@Query("SELECT e FROM Batch2JobInstanceEntity e WHERE e.myDefinitionId = :jobDefinitionId AND e.myStatus IN :statuses")
List<Batch2JobInstanceEntity> fetchInstancesByJobDefinitionIdAndStatus(@Param("jobDefinitionId") String theJobDefinitionId, @Param("statuses") Set<StatusEnum> theIncompleteStatuses, Pageable thePageRequest);
@Query("SELECT e FROM Batch2JobInstanceEntity e WHERE e.myDefinitionId = :jobDefinitionId")
List<Batch2JobInstanceEntity> findInstancesByJobDefinitionId(@Param("jobDefinitionId") String theJobDefinitionId, Pageable thePageRequest);
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/HSearchSortHelperImpl.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SortOrderEnum;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/IHSearchSortHelper.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.api.SortSpec;
import org.hibernate.search.engine.search.sort.dsl.SearchSortFactory;
import org.hibernate.search.engine.search.sort.dsl.SortFinalStep;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/ISynchronousSearchSvc.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.ISearchSvc;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SynchronousSearchSvcImpl.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.HookParams;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchHibernatePropertiesBuilder.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.elastic;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
import org.apache.commons.lang3.StringUtils;
@ -30,12 +30,12 @@ import org.elasticsearch.client.RequestOptions;
import org.elasticsearch.client.RestHighLevelClient;
import org.elasticsearch.client.indices.PutIndexTemplateRequest;
import org.elasticsearch.common.settings.Settings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings;
import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.slf4j.Logger;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/IndexNamePrefixLayoutStrategy.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.elastic;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SearchParameterMapCalculator.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.util;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.SummaryEnum;

70
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplTest.java Normal file
View File

@ -0,0 +1,70 @@
package ca.uhn.fhir.jpa.batch2;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.Optional;
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.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
class JpaJobPersistenceImplTest {
private static final String TEST_INSTANCE_ID = "test-instance-id";
@Mock
IBatch2JobInstanceRepository myJobInstanceRepository;
@Mock
IBatch2WorkChunkRepository myWorkChunkRepository;
@InjectMocks
JpaJobPersistenceImpl mySvc;
@Test
void cancelSuccess() {
// setup
when(myJobInstanceRepository.updateInstanceCancelled(TEST_INSTANCE_ID, true)).thenReturn(1);
// execute
JobOperationResultJson result = mySvc.cancelInstance(TEST_INSTANCE_ID);
// validate
assertTrue(result.getSuccess());
assertEquals("Job instance <test-instance-id> successfully cancelled.", result.getMessage());
}
@Test
void cancelNotFound() {
// setup
when(myJobInstanceRepository.updateInstanceCancelled(TEST_INSTANCE_ID, true)).thenReturn(0);
when(myJobInstanceRepository.findById(TEST_INSTANCE_ID)).thenReturn(Optional.empty());
// execute
JobOperationResultJson result = mySvc.cancelInstance(TEST_INSTANCE_ID);
// validate
assertFalse(result.getSuccess());
assertEquals("Job instance <test-instance-id> not found.", result.getMessage());
}
@Test
void cancelAlreadyCancelled() {
// setup
when(myJobInstanceRepository.updateInstanceCancelled(TEST_INSTANCE_ID, true)).thenReturn(0);
when(myJobInstanceRepository.findById(TEST_INSTANCE_ID)).thenReturn(Optional.of(new Batch2JobInstanceEntity()));
// execute
JobOperationResultJson result = mySvc.cancelInstance(TEST_INSTANCE_ID);
// validate
assertFalse(result.getSuccess());
assertEquals("Job instance <test-instance-id> was already cancelled. Nothing to do.", result.getMessage());
}
}

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/GoldenResourceSearchSvcImpl.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.mdm.svc;
/*-
* #%L
* HAPI FHIR JPA Server
* HAPI FHIR JPA Server - Master Data Management
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%

1
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java
View File

@ -23,7 +23,6 @@ import org.springframework.test.context.TestPropertySource;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.slf4j.LoggerFactory.getLogger;

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

31
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplTest.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.batch2;
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.batch2.coordinator.BatchWorkChunk;
import ca.uhn.fhir.batch2.jobs.imprt.NdJsonFileJson;
import ca.uhn.fhir.batch2.model.JobInstance;
@ -20,13 +21,16 @@ import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@ -136,7 +140,9 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
myJobInstanceRepository.save(instanceEntity);
});
mySvc.cancelInstance(instanceId);
JobOperationResultJson result = mySvc.cancelInstance(instanceId);
assertTrue(result.getSuccess());
assertEquals("Job instance <" + instanceId + "> successfully cancelled.", result.getMessage());
JobInstance foundInstance = mySvc.fetchInstanceAndMarkInProgress(instanceId).orElseThrow(() -> new IllegalStateException());
assertEquals(instanceId, foundInstance.getInstanceId());
@ -161,6 +167,29 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
assertEquals(CHUNK_DATA, foundInstance.getParameters());
}
@Test
void testFetchInstancesByJobDefinitionId() {
JobInstance instance = createInstance();
String instanceId = mySvc.storeNewInstance(instance);
List<JobInstance> foundInstances = mySvc.fetchInstancesByJobDefinitionId(JOB_DEFINITION_ID, 10, 0);
assertThat(foundInstances, hasSize(1));
assertEquals(instanceId, foundInstances.get(0).getInstanceId());
}
@Test
void testFetchInstancesByJobDefinitionIdAndStatus() {
JobInstance instance = createInstance();
String instanceId = mySvc.storeNewInstance(instance);
Set<StatusEnum> statuses = new HashSet<>();
statuses.add(StatusEnum.QUEUED);
statuses.add(StatusEnum.COMPLETED);
List<JobInstance> foundInstances = mySvc.fetchInstancesByJobDefinitionIdAndStatus(JOB_DEFINITION_ID, statuses, 10, 0);
assertThat(foundInstances, hasSize(1));
assertEquals(instanceId, foundInstances.get(0).getInstanceId());
}
@Test
public void testFetchChunks() {
JobInstance instance = createInstance();

4
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/config/ElasticsearchWithPrefixConfig.java
View File

@ -4,10 +4,11 @@ import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.r4.ElasticsearchPrefixTest;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
import ca.uhn.fhir.jpa.search.elastic.TestElasticsearchContainerHelper;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
@ -17,7 +18,6 @@ import org.elasticsearch.client.RequestOptions;
import org.elasticsearch.client.RestHighLevelClient;
import org.elasticsearch.client.indices.PutIndexTemplateRequest;
import org.elasticsearch.common.settings.Settings;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
View File

@ -4,11 +4,11 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.param.DateAndListParam;
import ca.uhn.fhir.rest.param.DateOrListParam;
import ca.uhn.fhir.rest.param.DateParam;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithHSearchDisabledTest.java
View File

@ -10,13 +10,13 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.util.ValueSetTestUtil;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyElasticsearchIT.java
View File

@ -7,7 +7,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -16,6 +15,7 @@ import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/PersistObservationIndexedSearchParamLastNR4IT.java
View File

@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
@ -11,6 +10,7 @@ import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/SyntheaPerfTest.java
View File

@ -3,12 +3,12 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.search.reindex.BlockPolicy;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.lang3.Validate;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/subscription/module/matcher/InMemorySubscriptionMatcherR4Test.java
View File

@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.subscription.module.matcher;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
@ -17,6 +16,7 @@ import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyE
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.util.CoordCalculatorTest;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.rest.param.CompositeParam;

7
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/AbstractValueSetHSearchExpansionR4Test.java
View File

@ -8,7 +8,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
@ -21,8 +20,7 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -46,15 +44,12 @@ import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Answers;
import org.mockito.Mock;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.test.util.AopTestUtils;
import org.springframework.test.util.ReflectionTestUtils;
import org.springframework.transaction.PlatformTransactionManager;

6
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java
View File

@ -8,9 +8,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -21,6 +18,9 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/hsearch/ReindexTerminologyHSearchR4Test.java
View File

@ -1,6 +1,5 @@
package ca.uhn.fhir.jpa.term.hsearch;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
@ -13,6 +12,7 @@ import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import net.ttddyy.dsproxy.ExecutionInfo;
import net.ttddyy.dsproxy.QueryInfo;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-server-mdm/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server-openapi/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<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
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage-batch2-jobs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

20
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexIdChunkProducer.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.reindex;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.jobs.step.IIdChunkProducer;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.pid.IResourcePidList;

2
hapi-fhir-storage-batch2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/ChunkExecutionDetails.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.api;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
public class ChunkExecutionDetails<PT extends IModelJson, IT extends IModelJson> {

8
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobCoordinator.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import javax.annotation.Nullable;
import java.util.List;
public interface IJobCoordinator {
@ -52,11 +53,14 @@ public interface IJobCoordinator {
*/
List<JobInstance> getInstances(int thePageSize, int thePageIndex);
/**
* Fetch job instances
* Fetch recent job instances
*/
List<JobInstance> getRecentInstances(int theCount, int theStart);
void cancelInstance(String theInstanceId) throws ResourceNotFoundException;
JobOperationResultJson cancelInstance(String theInstanceId) throws ResourceNotFoundException;
List<JobInstance> getInstancesbyJobDefinitionIdAndEndedStatus(String theJobDefinitionId, @Nullable Boolean theEnded, int theCount, int theStart);
}

15
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.batch2.model.WorkChunk;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
public interface IJobPersistence {
@ -83,6 +84,17 @@ public interface IJobPersistence {
*/
Optional<JobInstance> fetchInstanceAndMarkInProgress(String theInstanceId);
List<JobInstance> fetchInstancesByJobDefinitionIdAndStatus(String theJobDefinitionId, Set<StatusEnum> theRequestedStatuses, int thePageSize, int thePageIndex);
/**
* Fetch all job instances for a given job definition id
* @param theJobDefinitionId
* @param theCount
* @param theStart
* @return
*/
List<JobInstance> fetchInstancesByJobDefinitionId(String theJobDefinitionId, int theCount, int theStart);
/**
* Marks a given chunk as having errored (i.e. may be recoverable)
*
@ -172,6 +184,5 @@ public interface IJobPersistence {
*
* @param theInstanceId The instance ID
*/
void cancelInstance(String theInstanceId);
JobOperationResultJson cancelInstance(String theInstanceId);
}

53
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/JobOperationResultJson.java Normal file
View File

@ -0,0 +1,53 @@
package ca.uhn.fhir.batch2.api;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
public class JobOperationResultJson implements IModelJson {
@JsonProperty("operation")
private String myOperation;
@JsonProperty("success")
private Boolean mySuccess;
@JsonProperty("message")
private String myMessage;
public static JobOperationResultJson newSuccess(String theOperation, String theMessage) {
JobOperationResultJson result = new JobOperationResultJson();
result.setSuccess(true);
result.setOperation(theOperation);
result.setMessage(theMessage);
return result;
}
public static JobOperationResultJson newFailure(String theOperation, String theMessage) {
JobOperationResultJson result = new JobOperationResultJson();
result.setSuccess(false);
result.setOperation(theOperation);
result.setMessage(theMessage);
return result;
}
public String getOperation() {
return myOperation;
}
public void setOperation(String theOperation) {
myOperation = theOperation;
}
public Boolean getSuccess() {
return mySuccess;
}
public void setSuccess(Boolean theSuccess) {
mySuccess = theSuccess;
}
public String getMessage() {
return myMessage;
}
public void setMessage(String theMessage) {
myMessage = theMessage;
}
}

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/config/Batch2Constants.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.config;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.r4.model.InstantType;
import java.util.Date;

11
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/JobCoordinatorImpl.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.batch2.coordinator;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.batch2.channel.BatchJobSender;
import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.batch2.model.JobInstance;
@ -36,6 +37,7 @@ import org.apache.commons.lang3.Validate;
import org.springframework.messaging.MessageHandler;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import java.util.List;
@ -114,8 +116,13 @@ public class JobCoordinatorImpl implements IJobCoordinator {
}
@Override
public void cancelInstance(String theInstanceId) throws ResourceNotFoundException {
myJobPersistence.cancelInstance(theInstanceId);
public List<JobInstance> getInstancesbyJobDefinitionIdAndEndedStatus(String theJobDefinitionId, @Nullable Boolean theEnded, int theCount, int theStart) {
return myJobQuerySvc.getInstancesByJobDefinitionIdAndEndedStatus(theJobDefinitionId, theEnded, theCount, theStart);
}
@Override
public JobOperationResultJson cancelInstance(String theInstanceId) throws ResourceNotFoundException {
return myJobPersistence.cancelInstance(theInstanceId);
}
@PostConstruct

16
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/JobDefinitionRegistry.java
View File

@ -34,10 +34,12 @@ import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.TreeMap;
import java.util.stream.Collectors;
public class JobDefinitionRegistry {
private static final Logger ourLog = LoggerFactory.getLogger(JobDefinitionRegistry.class);
@ -114,4 +116,18 @@ public class JobDefinitionRegistry {
JobDefinition<?> jobDefinition = getJobDefinitionOrThrowException(theInstance.getJobDefinitionId(), theInstance.getJobDefinitionVersion());
theInstance.setJobDefinition(jobDefinition);
}
/**
* @return a list of Job Definition Ids in alphabetical order
*/
public List<String> getJobDefinitionIds() {
return myJobs.keySet()
.stream()
.sorted()
.collect(Collectors.toList());
}
public boolean isEmpty() {
return myJobs.isEmpty();
}
}

26
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/JobQuerySvc.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.batch2.coordinator;
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IModelJson;
import ca.uhn.fhir.model.api.annotation.PasswordField;
@ -33,8 +34,10 @@ import ca.uhn.fhir.util.UrlUtil;
import com.fasterxml.jackson.annotation.JsonProperty;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.lang.reflect.Field;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
/**
@ -62,8 +65,12 @@ class JobQuerySvc {
}
public List<JobInstance> fetchRecentInstances(int theCount, int theStart) {
return myJobPersistence.fetchRecentInstances(theCount, theStart)
.stream().map(this::massageInstanceForUserAccess)
return massageInstancesForUserAccess(myJobPersistence.fetchRecentInstances(theCount, theStart));
}
private List<JobInstance> massageInstancesForUserAccess(List<JobInstance> theFetchRecentInstances) {
return theFetchRecentInstances.stream()
.map(this::massageInstanceForUserAccess)
.collect(Collectors.toList());
}
@ -107,4 +114,19 @@ class JobQuerySvc {
}
}
}
public List<JobInstance> getInstancesByJobDefinitionIdAndEndedStatus(String theJobDefinitionId, @Nullable Boolean theEnded, int theCount, int theStart) {
if (theEnded == null) {
return myJobPersistence.fetchInstancesByJobDefinitionId(theJobDefinitionId, theCount, theStart);
}
Set<StatusEnum> requestedStatus;
if (theEnded) {
requestedStatus = StatusEnum.getEndedStatuses();
} else {
requestedStatus = StatusEnum.getNotEndedStatuses();
}
return myJobPersistence.fetchInstancesByJobDefinitionIdAndStatus(theJobDefinitionId, requestedStatus, theCount, theStart);
}
}

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/JobStepExecutorOutput.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.coordinator;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
public class JobStepExecutorOutput<PT extends IModelJson, IT extends IModelJson, OT extends IModelJson> {

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/ReductionStepDataSink.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.coordinator;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.model.JobDefinition;

21
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/StepExecutionSvc.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.coordinator;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.api.ChunkExecutionDetails;
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
@ -26,7 +46,6 @@ import org.slf4j.LoggerFactory;
import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;

16
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/SynchronizedJobPersistenceWrapper.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.batch2.coordinator;
*/
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
@ -28,6 +29,7 @@ import ca.uhn.fhir.batch2.model.WorkChunk;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
public class SynchronizedJobPersistenceWrapper implements IJobPersistence {
@ -75,6 +77,16 @@ public class SynchronizedJobPersistenceWrapper implements IJobPersistence {
return myWrap.fetchInstanceAndMarkInProgress(theInstanceId);
}
@Override
public List<JobInstance> fetchInstancesByJobDefinitionIdAndStatus(String theJobDefinitionId, Set<StatusEnum> theRequestedStatuses, int thePageSize, int thePageIndex) {
return myWrap.fetchInstancesByJobDefinitionIdAndStatus(theJobDefinitionId, theRequestedStatuses, thePageSize, thePageIndex);
}
@Override
public List<JobInstance> fetchInstancesByJobDefinitionId(String theJobDefinitionId, int theCount, int theStart) {
return myWrap.fetchInstancesByJobDefinitionId(theJobDefinitionId, theCount, theStart);
}
@Override
public synchronized void markWorkChunkAsErroredAndIncrementErrorCount(String theChunkId, String theErrorMessage) {
myWrap.markWorkChunkAsErroredAndIncrementErrorCount(theChunkId, theErrorMessage);
@ -132,7 +144,7 @@ public class SynchronizedJobPersistenceWrapper implements IJobPersistence {
}
@Override
public void cancelInstance(String theInstanceId) {
myWrap.cancelInstance(theInstanceId);
public JobOperationResultJson cancelInstance(String theInstanceId) {
return myWrap.cancelInstance(theInstanceId);
}
}

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/chunk/ChunkRangeJson.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.chunk;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.util.JsonDateDeserializer;
import ca.uhn.fhir.jpa.util.JsonDateSerializer;
import ca.uhn.fhir.model.api.IModelJson;

2
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/chunk/ResourceIdListWorkChunkJson.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.batch2.jobs.chunk;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/chunk/TypedPidJson.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.chunk;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.pid.TypedResourcePid;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/parameters/PartitionedJobParameters.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.parameters;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/step/IIdChunkProducer.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.step;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.jobs.chunk.ChunkRangeJson;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.pid.IResourcePidList;

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/jobs/step/ResourceIdListStep.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.step;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/ChunkOutcome.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.model;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class ChunkOutcome {
public enum Status {
SUCCESS,

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/JobDefinitionReductionStep.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.model;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.IReductionStepWorker;
import ca.uhn.fhir.model.api.IModelJson;

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/ListResult.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.model;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

67
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/StatusEnum.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.batch2.model;
* #L%
*/
import javax.annotation.Nonnull;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Set;
@ -29,40 +30,44 @@ public enum StatusEnum {
/**
* Task is waiting to execute and should begin with no intervention required.
*/
QUEUED(true),
QUEUED(true, false),
/**
* Task is current executing
*/
IN_PROGRESS(true),
IN_PROGRESS(true, false),
/**
* Task completed successfully
*/
COMPLETED(false),
COMPLETED(false, true),
/**
* Task execution resulted in an error but the error may be transient (or transient status is unknown).
* Retrying may result in success.
*/
ERRORED(true),
ERRORED(true, true),
/**
* Task has failed and is known to be unrecoverable. There is no reason to believe that retrying will
* result in a different outcome.
*/
FAILED(true),
FAILED(true, true),
/**
* Task has been cancelled.
*/
CANCELLED(true);
CANCELLED(true, true);
private final boolean myIncomplete;
private final boolean myEnded;
private static Set<StatusEnum> ourIncompleteStatuses;
private static Set<StatusEnum> ourEndedStatuses;
private static Set<StatusEnum> ourNotEndedStatuses;
StatusEnum(boolean theIncomplete) {
StatusEnum(boolean theIncomplete, boolean theEnded) {
myIncomplete = theIncomplete;
myEnded = theEnded;
}
/**
@ -72,16 +77,58 @@ public enum StatusEnum {
public static Set<StatusEnum> getIncompleteStatuses() {
Set<StatusEnum> retVal = ourIncompleteStatuses;
if (retVal == null) {
EnumSet<StatusEnum> set = EnumSet.noneOf(StatusEnum.class);
EnumSet<StatusEnum> incompleteSet = EnumSet.noneOf(StatusEnum.class);
for (StatusEnum next : values()) {
if (next.myIncomplete) {
set.add(next);
incompleteSet.add(next);
}
}
ourIncompleteStatuses = Collections.unmodifiableSet(set);
ourIncompleteStatuses = Collections.unmodifiableSet(incompleteSet);
retVal = ourIncompleteStatuses;
}
return retVal;
}
/**
* Statuses that represent a job that has ended. I.e.
* all statuses except {@link #QUEUED and #COMPLETED}
*/
@Nonnull
public static Set<StatusEnum> getEndedStatuses() {
Set<StatusEnum> retVal = ourEndedStatuses;
if (retVal == null) {
initializeStaticEndedStatuses();
}
retVal = ourEndedStatuses;
return retVal;
}
/**
* Statuses that represent a job that has not ended. I.e.
* {@link #QUEUED and #COMPLETED}
*/
@Nonnull
public static Set<StatusEnum> getNotEndedStatuses() {
Set<StatusEnum> retVal = ourNotEndedStatuses;
if (retVal == null) {
initializeStaticEndedStatuses();
}
retVal = ourNotEndedStatuses;
return retVal;
}
@Nonnull
private static void initializeStaticEndedStatuses() {
EnumSet<StatusEnum> endedSet = EnumSet.noneOf(StatusEnum.class);
EnumSet<StatusEnum> notEndedSet = EnumSet.noneOf(StatusEnum.class);
for (StatusEnum next : values()) {
if (next.myEnded) {
endedSet.add(next);
} else {
notEndedSet.add(next);
}
}
ourEndedStatuses = Collections.unmodifiableSet(endedSet);
ourNotEndedStatuses = Collections.unmodifiableSet(notEndedSet);
}
}

17
hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/model/StatusEnumTest.java Normal file
View File

@ -0,0 +1,17 @@
package ca.uhn.fhir.batch2.model;
import org.junit.jupiter.api.Test;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
class StatusEnumTest {
@Test
public void testEndedStatuses() {
assertThat(StatusEnum.getEndedStatuses(), containsInAnyOrder(StatusEnum.COMPLETED, StatusEnum.FAILED, StatusEnum.CANCELLED, StatusEnum.ERRORED));
}
@Test
public void testNotEndedStatuses() {
assertThat(StatusEnum.getNotEndedStatuses(), containsInAnyOrder(StatusEnum.QUEUED, StatusEnum.IN_PROGRESS));
}
}

2
hapi-fhir-storage-mdm/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE5-SNAPSHOT</version>
<version>6.1.0-PRE6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/LoadGoldenIdsStep.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.mdm.batch2;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* hapi-fhir-storage-mdm
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%

20
hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/MdmBatch2Config.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.mdm.batch2;
/*-
* #%L
* hapi-fhir-storage-mdm
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.mdm.batch2.clear.MdmClearAppCtx;

2
hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/MdmChunkRangeJson.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.mdm.batch2;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* hapi-fhir-storage-mdm
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%

2
hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/MdmGenerateRangeChunksStep.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.mdm.batch2;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* hapi-fhir-storage-mdm
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%

20
hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/MdmIdChunkProducer.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.mdm.batch2;
/*-
* #%L
* hapi-fhir-storage-mdm
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.batch2.jobs.step.IIdChunkProducer;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.pid.IResourcePidList;

2
hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/clear/MdmClearAppCtx.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.mdm.batch2.clear;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* hapi-fhir-storage-mdm
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%

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