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hapi-fhir
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remove spring batch (#4064) 

* remove spring batch
it compiles
expect test failures

* fix test transaction manager bean name (wow that was quite the hunt the wumpus!)

* fix test and fix build

* fix test and fix build

* fix test

* remove spring batch schema initialization

* bump hapi version

* fix schema migrator

* bump to PRE-10

* merge master

* change logs

Co-authored-by: Ken Stevens <ken@smilecdr.com>
This commit is contained in:
Ken Stevens 2022-09-30 13:18:48 -04:00 committed by GitHub
parent b472c4bb54
commit e9a855d3f6
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
123 changed files with 138 additions and 1486 deletions
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2
azure-pipelines.yml
View File

@ -36,8 +36,6 @@ stages:
module: hapi-fhir-android
- name: hapi_fhir_base
module: hapi-fhir-base
- name: hapi_fhir_batch
module: hapi-fhir-batch
- name: hapi_fhir_checkstyle
module: hapi-fhir-checkstyle
- name: hapi_fhir_cli_api

2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

43
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/api/IBatchJobSubmitter.java
View File

@ -1,43 +0,0 @@
package ca.uhn.fhir.jpa.batch.api;
/*-
* #%L
* HAPI FHIR JPA Server - Batch 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.springframework.batch.core.Job;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
/**
* @deprecated use IJobCoordinator instead
*/
@Deprecated
public interface IBatchJobSubmitter {
/**
* Given a {@link Job} and a {@link JobParameters}, execute the job with the given parameters.
*
* @param theJob the job to run.
* @param theJobParameters A collection of key-value pairs that are used to parameterize the job.
* @return A {@link JobExecution} representing the job.
* @throws JobParametersInvalidException If validation on the parameters fails.
*/
JobExecution runJob(Job theJob, JobParameters theJobParameters) throws JobParametersInvalidException;
}

112
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/BatchConstants.java
View File

@ -1,112 +0,0 @@
package ca.uhn.fhir.jpa.batch.config;
/*-
* #%L
* HAPI FHIR JPA Server - Batch 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 java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
public final class BatchConstants {
public static final String JOB_PARAM_REQUEST_LIST = "url-list";
public static final String JOB_PARAM_BATCH_SIZE = "batch-size";
public static final String JOB_PARAM_START_TIME = "start-time";
public static final String CURRENT_URL_INDEX = "current.url-index";
public static final String CURRENT_THRESHOLD_HIGH = "current.threshold-high";
public static final String JOB_UUID_PARAMETER = "jobUUID";
public static final String JOB_LAUNCHING_TASK_EXECUTOR = "jobLaunchingTaskExecutor";
public static final String BULK_EXPORT_JOB_NAME = "bulkExportJob";
public static final String GROUP_BULK_EXPORT_JOB_NAME = "groupBulkExportJob";
public static final String PATIENT_BULK_EXPORT_JOB_NAME = "patientBulkExportJob";
public static final String BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP = "bulkExportGenerateResourceFilesStep";
public static final String BULK_IMPORT_JOB_NAME = "bulkImportJob";
public static final String BULK_IMPORT_PROCESSING_STEP = "bulkImportProcessingStep";
/**
* Delete Expunge
*/
public static final String DELETE_EXPUNGE_JOB_NAME = "deleteExpungeJob";
/**
* MDM Clear
*/
public static final String MDM_CLEAR_JOB_NAME = "mdmClearJob";
/**
* TermCodeSystem delete
*/
public static final String TERM_CODE_SYSTEM_DELETE_JOB_NAME = "termCodeSystemDeleteJob";
/**
* TermCodeSystemVersion delete
*/
public static final String TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME = "termCodeSystemVersionDeleteJob";
/**
* Both: TermCodeSystem delete and TermCodeSystemVersion delete
*/
public static final String JOB_PARAM_CODE_SYSTEM_VERSION_ID = "termCodeSystemVersionPid";
public static final String BULK_EXPORT_READ_CHUNK_PARAMETER = "readChunkSize";
public static final String BULK_EXPORT_GROUP_ID_PARAMETER = "groupId";
/**
* Job Parameters
*/
public static final String READ_CHUNK_PARAMETER = "readChunkSize";
public static final String EXPAND_MDM_PARAMETER = "expandMdm";
public static final String GROUP_ID_PARAMETER = "groupId";
public static final String JOB_RESOURCE_TYPES_PARAMETER = "resourceTypes";
public static final String JOB_DESCRIPTION = "jobDescription";
public static final String JOB_SINCE_PARAMETER = "since";
public static final String JOB_TYPE_FILTERS = "filters";
public static final String JOB_COLLECTION_ENTITY_ID = "bulkExportCollectionEntityId";
/**
* Job Execution Context
*/
public static final String JOB_EXECUTION_RESOURCE_TYPE = "resourceType";
public static final List<String> PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES = List.of("Practitioner", "Organization");
/**
* This Set contains the step names across all job types that are appropriate for
* someone to look at the write count for that given step in order to determine the
* number of processed records.
* <p>
* This is provided since a job might have multiple steps that the same data passes
* through, so you can't just sum up the total of all of them.
* <p>
* For any given batch job type, there should only be one step name in this set
*/
public static Set<String> RECORD_PROCESSING_STEP_NAMES;
static {
HashSet<String> recordProcessingStepNames = new HashSet<>();
recordProcessingStepNames.add(BatchConstants.BULK_IMPORT_PROCESSING_STEP);
recordProcessingStepNames.add(BatchConstants.BULK_EXPORT_GENERATE_RESOURCE_FILES_STEP);
BatchConstants.RECORD_PROCESSING_STEP_NAMES = Collections.unmodifiableSet(recordProcessingStepNames);
}
/**
* v * Non instantiable
*/
private BatchConstants() {
}
}

76
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/NonPersistedBatchConfigurer.java
View File

@ -1,76 +0,0 @@
package ca.uhn.fhir.jpa.batch.config;
/*-
* #%L
* HAPI FHIR JPA Server - Batch 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.springframework.batch.core.configuration.annotation.DefaultBatchConfigurer;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.explore.support.MapJobExplorerFactoryBean;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.SimpleJobLauncher;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.batch.core.repository.support.MapJobRepositoryFactoryBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.core.task.TaskExecutor;
import org.springframework.transaction.PlatformTransactionManager;
public class NonPersistedBatchConfigurer extends DefaultBatchConfigurer {
@Autowired
@Qualifier("hapiTransactionManager")
private PlatformTransactionManager myHapiPlatformTransactionManager;
@Autowired
@Qualifier(BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
private TaskExecutor myTaskExecutor;
private MapJobRepositoryFactoryBean myJobRepositoryFactory;
@Override
public PlatformTransactionManager getTransactionManager() {
return myHapiPlatformTransactionManager;
}
@Override
protected JobRepository createJobRepository() throws Exception {
MapJobRepositoryFactoryBean factory = new MapJobRepositoryFactoryBean();
factory.setTransactionManager(this.getTransactionManager());
factory.afterPropertiesSet();
myJobRepositoryFactory = factory;
return factory.getObject();
}
@Override
public JobExplorer createJobExplorer() throws Exception {
MapJobExplorerFactoryBean jobExplorerFactoryBean = new MapJobExplorerFactoryBean(myJobRepositoryFactory);
jobExplorerFactoryBean.afterPropertiesSet();
return jobExplorerFactoryBean.getObject();
}
@Override
protected JobLauncher createJobLauncher() throws Exception {
SimpleJobLauncher launcher = new SimpleJobLauncher();
launcher.setTaskExecutor(myTaskExecutor);
launcher.setJobRepository(getJobRepository());
launcher.afterPropertiesSet();
return launcher;
}
}

67
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/svc/BatchJobSubmitterImpl.java
View File

@ -1,67 +0,0 @@
package ca.uhn.fhir.jpa.batch.svc;
/*-
* #%L
* HAPI FHIR JPA Server - Batch 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.batch.api.IBatchJobSubmitter;
import org.slf4j.Logger;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.repository.JobExecutionAlreadyRunningException;
import org.springframework.batch.core.repository.JobInstanceAlreadyCompleteException;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.batch.core.repository.JobRestartException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Propagation;
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);
@Autowired
private JobLauncher myJobLauncher;
@Autowired
private JobRepository myJobRepository;
@Override
@Transactional(propagation = Propagation.NOT_SUPPORTED)
public JobExecution runJob(Job theJob, JobParameters theJobParameters) throws JobParametersInvalidException {
try {
return myJobLauncher.run(theJob, theJobParameters);
} catch (JobExecutionAlreadyRunningException | JobRestartException | JobInstanceAlreadyCompleteException e) {
ourLog.warn("Job {} was already running, ignoring the call to start: {}", theJob.getName(), e.toString());
return myJobRepository.getLastJobExecution(theJob.getName(), theJobParameters);
} catch (JobParametersInvalidException e) {
ourLog.error("Job Parameters passed to this job were invalid: {}", e.getMessage());
throw e;
}
}
}

12
hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/BaseBatchR4Test.java
View File

@ -1,12 +0,0 @@
package ca.uhn.fhir.jpa.batch;
import ca.uhn.fhir.jpa.batch.config.BatchJobConfig;
import ca.uhn.fhir.jpa.batch.config.TestBatchConfig;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {BatchJobConfig.class, TestBatchConfig.class})
abstract public class BaseBatchR4Test {
}

54
hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/config/BatchJobConfig.java
View File

@ -1,54 +0,0 @@
package ca.uhn.fhir.jpa.batch.config;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class BatchJobConfig {
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Autowired
private StepBuilderFactory myStepBuilderFactory;
@Bean
public Job testJob() {
return myJobBuilderFactory.get("testJob")
.start(testStep())
.build();
}
@Bean
public Step testStep() {
return myStepBuilderFactory.get("testStep")
.tasklet(sampleTasklet())
.build();
}
@Bean
@StepScope
public Tasklet sampleTasklet() {
return new SampleTasklet();
}
@Bean
@StepScope
public SampleItemReader reader() {
return new SampleItemReader();
}
@Bean
public ItemWriter<String> simpleWriter() {
return theList -> theList.forEach(System.out::println);
}
}

15
hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/config/SampleItemReader.java
View File

@ -1,15 +0,0 @@
package ca.uhn.fhir.jpa.batch.config;
import org.springframework.batch.item.ItemReader;
import org.springframework.batch.item.NonTransientResourceException;
import org.springframework.batch.item.ParseException;
import org.springframework.batch.item.UnexpectedInputException;
public class SampleItemReader implements ItemReader<String> {
@Override
public String read() throws Exception, UnexpectedInputException, ParseException, NonTransientResourceException {
return "zoop";
}
}

14
hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/config/SampleTasklet.java
View File

@ -1,14 +0,0 @@
package ca.uhn.fhir.jpa.batch.config;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
public class SampleTasklet implements Tasklet {
@Override
public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) throws Exception {
System.out.println("woo");
return RepeatStatus.FINISHED;
}
}

36
hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/config/TestBatchConfig.java
View File

@ -1,36 +0,0 @@
package ca.uhn.fhir.jpa.batch.config;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.support.transaction.ResourcelessTransactionManager;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.task.TaskExecutor;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.transaction.PlatformTransactionManager;
@Configuration
@EnableBatchProcessing
public class TestBatchConfig {
@Bean
public PlatformTransactionManager hapiTransactionManager() {
return new ResourcelessTransactionManager();
}
@Bean
public TaskExecutor jobLaunchingTaskExecutor() {
ThreadPoolTaskExecutor asyncTaskExecutor = new ThreadPoolTaskExecutor();
asyncTaskExecutor.setCorePoolSize(5);
asyncTaskExecutor.setMaxPoolSize(10);
asyncTaskExecutor.setQueueCapacity(500);
asyncTaskExecutor.setThreadNamePrefix("JobLauncher-");
asyncTaskExecutor.initialize();
return asyncTaskExecutor;
}
@Bean
public BatchConfigurer batchConfigurer() {
return new NonPersistedBatchConfigurer();
}
}

24
hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/svc/BatchSvcTest.java
View File

@ -1,24 +0,0 @@
package ca.uhn.fhir.jpa.batch.svc;
import ca.uhn.fhir.jpa.batch.BaseBatchR4Test;
import org.junit.jupiter.api.Test;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.repository.JobExecutionAlreadyRunningException;
import org.springframework.batch.core.repository.JobInstanceAlreadyCompleteException;
import org.springframework.batch.core.repository.JobRestartException;
import org.springframework.beans.factory.annotation.Autowired;
public class BatchSvcTest extends BaseBatchR4Test {
@Autowired
protected JobLauncher myJobLauncher;
@Autowired
protected Job myJob;
@Test
public void testApplicationContextLoads() throws JobParametersInvalidException, JobExecutionAlreadyRunningException, JobRestartException, JobInstanceAlreadyCompleteException, InterruptedException {
myJobLauncher.run(myJob, new JobParameters());
}
}

78
hapi-fhir-batch/src/test/resources/logback-test.xml
View File

@ -1,78 +0,0 @@
<configuration>
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
</encoder>
</appender>
<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false"
level="info">
<appender-ref ref="STDOUT"/>
</logger>
<logger name="ca.uhn.fhir.jpa.dao.FhirResourceDaoSubscriptionDstu2" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<logger name="org.eclipse.jetty.websocket" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<logger name="org.eclipse" additivity="false" level="error">
</logger>
<logger name="ca.uhn.fhir.rest.client" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<logger name="ca.uhn.fhir.jpa.dao" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<!-- Set to 'trace' to enable SQL logging -->
<logger name="org.hibernate.SQL" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<!-- Set to 'trace' to enable SQL Value logging -->
<logger name="org.hibernate.type" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="trace">
<appender-ref ref="STDOUT"/>
</logger>
<logger name="org.hibernate" additivity="false" level="info">
<appender-ref ref="STDOUT"/>
</logger>
<appender name="BATCH_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
</filter>
<file>${smile.basedir}/log/batch-troubleshooting.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
<fileNamePattern>${smile.basedir}/log/batch-troubleshooting.log.%i.gz</fileNamePattern>
<minIndex>1</minIndex>
<maxIndex>9</maxIndex>
</rollingPolicy>
<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
<maxFileSize>5MB</maxFileSize>
</triggeringPolicy>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}
</pattern>
</encoder>
</appender>
<logger name="ca.uhn.fhir.log.batch_troubleshooting" level="TRACE">
<appender-ref ref="BATCH_TROUBLESHOOTING"/>
</logger>
<root level="info">
<appender-ref ref="STDOUT"/>
</root>
</configuration>

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3546-remove-spring-batch.yaml Normal file
View File

@ -0,0 +1,3 @@
---
type: change
title: "All Spring Batch dependencies and services have been removed. Async processing has fully migrated to Batch 2."

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java
View File

@ -1,68 +0,0 @@
package ca.uhn.fhir.jpa.batch;
/*-
* #%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.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
import ca.uhn.fhir.jpa.config.BatchJobRegisterer;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.SimpleJobOperator;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@Configuration
@EnableBatchProcessing
@Import({
CommonBatchJobConfig.class
// When you define a new batch job, add it here.
})
@Deprecated
/**
* @deprecated Use Batch2JobsConfig
*/
public class BatchJobsConfig {
@Bean
public IBatchJobSubmitter batchJobSubmitter() {
return new BatchJobSubmitterImpl();
}
@Bean
public BatchJobRegisterer batchJobRegisterer() {
return new BatchJobRegisterer();
}
@Bean
public SimpleJobOperator jobOperator(JobExplorer theJobExplorer, JobRepository theJobRepository, JobRegistry theJobRegistry, JobLauncher theJobLauncher) {
SimpleJobOperator jobOperator = new SimpleJobOperator();
jobOperator.setJobExplorer(theJobExplorer);
jobOperator.setJobRepository(theJobRepository);
jobOperator.setJobRegistry(theJobRegistry);
jobOperator.setJobLauncher(theJobLauncher);
return jobOperator;
}
}

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/CommonBatchJobConfig.java
View File

@ -1,39 +0,0 @@
package ca.uhn.fhir.jpa.batch;
/*-
* #%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.batch.processor.GoldenResourceAnnotatingProcessor;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
@Deprecated
public class CommonBatchJobConfig {
public static final int MINUTES_IN_FUTURE_TO_PROCESS_FROM = 1;
@Bean
@StepScope
public GoldenResourceAnnotatingProcessor goldenResourceAnnotatingProcessor() {
return new GoldenResourceAnnotatingProcessor();
}
}

168
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processor/GoldenResourceAnnotatingProcessor.java
View File

@ -1,168 +0,0 @@
package ca.uhn.fhir.jpa.batch.processor;
/*-
* #%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.context.RuntimeSearchParam;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.util.ExtensionUtil;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.SearchParameterUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import javax.annotation.Nonnull;
import java.util.List;
import java.util.Optional;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
/**
* Reusable Item Processor which attaches an extension to any outgoing resource. This extension will contain a resource
* reference to the golden resource patient of the given resources' patient. (e.g. Observation.subject, Immunization.patient, etc)
*/
@Deprecated
public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBaseResource>, List<IBaseResource>> {
private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
@Value("#{stepExecutionContext['resourceType']}")
private String myResourceType;
@Autowired
private FhirContext myContext;
@Autowired
private MdmExpansionCacheSvc myMdmExpansionCacheSvc;
@Value("#{jobParameters['" + BatchConstants.EXPAND_MDM_PARAMETER + "'] ?: false}")
private boolean myMdmEnabled;
private RuntimeSearchParam myRuntimeSearchParam;
private String myPatientFhirPath;
private IFhirPath myFhirPath;
private void populateRuntimeSearchParam() {
Optional<RuntimeSearchParam> oPatientSearchParam= SearchParameterUtil.getOnlyPatientSearchParamForResourceType(myContext, myResourceType);
if (!oPatientSearchParam.isPresent()) {
String errorMessage = String.format("[%s] has no search parameters that are for patients, so it is invalid for Group Bulk Export!", myResourceType);
throw new IllegalArgumentException(Msg.code(1279) + errorMessage);
} else {
myRuntimeSearchParam = oPatientSearchParam.get();
}
}
@Override
public List<IBaseResource> process(@Nonnull List<IBaseResource> theIBaseResources) throws Exception {
if (shouldAnnotateResource()) {
lazyLoadSearchParamsAndFhirPath();
theIBaseResources.forEach(this::annotateBackwardsReferences);
}
return theIBaseResources;
}
private void lazyLoadSearchParamsAndFhirPath() {
if (myRuntimeSearchParam == null) {
populateRuntimeSearchParam();
}
if (myPatientFhirPath == null) {
populatePatientFhirPath();
}
}
/**
* If the resource is added via a forward-reference from a patient, e.g. Patient.managingOrganization, we have no way to fetch the patient at this point in time.
* This is a shortcoming of including the forward reference types in a Group/Patient bulk export.
*
* @return true if the resource should be annotated with the golden resource patient reference
*/
private boolean shouldAnnotateResource() {
return myMdmEnabled && !PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType);
}
private void annotateBackwardsReferences(IBaseResource iBaseResource) {
Optional<String> patientReference = getPatientReference(iBaseResource);
if (patientReference.isPresent()) {
addGoldenResourceExtension(iBaseResource, patientReference.get());
} else {
ourLog.error("Failed to find the patient reference information for resource {}. This is a bug, " +
"as all resources which can be exported via Group Bulk Export must reference a patient.", iBaseResource);
}
}
private Optional<String> getPatientReference(IBaseResource iBaseResource) {
if (myResourceType.equalsIgnoreCase("Patient")) {
return Optional.of(iBaseResource.getIdElement().getIdPart());
} else {
Optional<IBaseReference> optionalReference = getFhirParser().evaluateFirst(iBaseResource, myPatientFhirPath, IBaseReference.class);
if (optionalReference.isPresent()) {
return optionalReference.map(theIBaseReference -> theIBaseReference.getReferenceElement().getIdPart());
} else {
return Optional.empty();
}
}
}
private void addGoldenResourceExtension(IBaseResource iBaseResource, String sourceResourceId) {
String goldenResourceId = myMdmExpansionCacheSvc.getGoldenResourceId(sourceResourceId);
IBaseExtension<?, ?> extension = ExtensionUtil.getOrCreateExtension(iBaseResource, HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL);
if (!StringUtils.isBlank(goldenResourceId)) {
ExtensionUtil.setExtension(myContext, extension, "reference", prefixPatient(goldenResourceId));
}
}
private String prefixPatient(String theResourceId) {
return "Patient/" + theResourceId;
}
private IFhirPath getFhirParser() {
if (myFhirPath == null) {
myFhirPath = myContext.newFhirPath();
}
return myFhirPath;
}
private String populatePatientFhirPath() {
if (myPatientFhirPath == null) {
myPatientFhirPath = myRuntimeSearchParam.getPath();
// GGG: Yes this is a stupid hack, but by default this runtime search param will return stuff like
// Observation.subject.where(resolve() is Patient) which unfortunately our FHIRpath evaluator doesn't play nicely with
// our FHIRPath evaluator.
if (myPatientFhirPath.contains(".where")) {
myPatientFhirPath = myPatientFhirPath.substring(0, myPatientFhirPath.indexOf(".where"));
}
}
return myPatientFhirPath;
}
}

73
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParametersBuilder.java
View File

@ -1,73 +0,0 @@
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%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.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.api.Constants;
import org.springframework.batch.core.JobParametersBuilder;
import java.util.Date;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
/**
* This builder is a helper so you don't have to go lookup what job parameters are required for a bulk export job.
*
*/
public class BulkExportJobParametersBuilder extends JobParametersBuilder {
public BulkExportJobParametersBuilder setResourceTypes(List<String> resourceTypes) {
String resourceTypesString = resourceTypes.stream().collect(Collectors.joining(","));
this.addString("resourceTypes", resourceTypesString);
return this;
}
public BulkExportJobParametersBuilder setSince(Date theSince) {
this.addDate("since", theSince);
return this;
}
public BulkExportJobParametersBuilder setOutputFormat(String theOutputFormat) {
//TODO eventually we will support more types.
theOutputFormat = Constants.CT_FHIR_NDJSON;
this.addString("outputFormat", theOutputFormat);
return this;
}
public BulkExportJobParametersBuilder setFilters(Set<String> theFilters) {
this.addString("filters", theFilters.stream().collect(Collectors.joining(",")));
return this;
}
public BulkExportJobParametersBuilder setJobUUID(String theJobUUID) {
this.addString("jobUUID", theJobUUID);
return this;
}
public BulkExportJobParametersBuilder setReadChunkSize(Long theReadChunkSize) {
this.addLong("readChunkSize", theReadChunkSize);
return this;
}
public BulkExportJobParametersBuilder setExportStyle(BulkDataExportOptions.ExportStyle theExportStyle) {
this.addString("exportStyle", theExportStyle.name());
return this;
}
}

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkExportJobParametersBuilder.java
View File

@ -1,35 +0,0 @@
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%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.batch.config.BatchConstants;
public class GroupBulkExportJobParametersBuilder extends BulkExportJobParametersBuilder {
public GroupBulkExportJobParametersBuilder setGroupId(String theGroupId) {
this.addString(BatchConstants.GROUP_ID_PARAMETER, theGroupId);
return this;
}
public GroupBulkExportJobParametersBuilder setMdm(boolean theMdm) {
this.addString(BatchConstants.EXPAND_MDM_PARAMETER, String.valueOf(theMdm));
return this;
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportJobSchedulingHelperImpl.java
View File

@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
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.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
@ -62,9 +61,6 @@ public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJob
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private IBatchJobSubmitter myJobSubmitter;
@Autowired
private IBulkExportCollectionDao myBulkExportCollectionDao;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java
View File

@ -24,7 +24,6 @@ import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.importpull.models.Batch2BulkImportPullJobParameters;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.ActivateJobResult;
@ -61,6 +60,8 @@ import java.util.Optional;
import java.util.UUID;
import java.util.concurrent.Semaphore;
import static ca.uhn.fhir.batch2.jobs.importpull.BulkImportPullConfig.BULK_IMPORT_JOB_NAME;
public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
private static final Logger ourLog = LoggerFactory.getLogger(BulkDataImportSvcImpl.class);
private final Semaphore myRunningJobSemaphore = new Semaphore(1);
@ -285,7 +286,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
jobParameters.setBatchSize(batchSize);
JobInstanceStartRequest request = new JobInstanceStartRequest();
request.setJobDefinitionId(BatchConstants.BULK_IMPORT_JOB_NAME);
request.setJobDefinitionId(BULK_IMPORT_JOB_NAME);
request.setParameters(jobParameters);
ourLog.info("Submitting bulk import with bijob id {} to job scheduler", biJobId);

61
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BatchJobRegisterer.java
View File

@ -1,61 +0,0 @@
package ca.uhn.fhir.jpa.config;
/*-
* #%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 org.springframework.batch.core.Job;
import org.springframework.batch.core.configuration.DuplicateJobException;
import org.springframework.batch.core.configuration.JobFactory;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import javax.annotation.PostConstruct;
import java.util.Map;
public class BatchJobRegisterer {
@Autowired
private ApplicationContext myApplicationContext;
@PostConstruct
public void start() throws DuplicateJobException {
Map<String, Job> batchJobs = myApplicationContext.getBeansOfType(Job.class);
JobRegistry jobRegistry = myApplicationContext.getBean(JobRegistry.class);
for (Map.Entry<String, Job> next : batchJobs.entrySet()) {
jobRegistry.register(new JobFactory() {
@Override
public Job createJob() {
return next.getValue();
}
@Override
public String getJobName() {
return next.getKey();
}
});
}
}
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiJpaConfig.java
View File

@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.api.IDaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
@ -40,7 +39,6 @@ import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -75,11 +73,6 @@ public class HapiJpaConfig {
return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
}
@Bean
public BatchConfigurer batchConfigurer() {
return new NonPersistedBatchConfigurer();
}
@Bean
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
return new DatabaseBackedPagingProvider();

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -10,8 +10,6 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
@ -74,7 +72,6 @@ import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
import ca.uhn.fhir.jpa.search.SearchStrategyFactory;
import ca.uhn.fhir.jpa.search.SynchronousSearchSvcImpl;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.search.builder.tasks.SearchTask;
import ca.uhn.fhir.jpa.search.builder.predicate.ComboNonUniqueSearchParameterPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ComboUniqueSearchParameterPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder;
@ -96,6 +93,7 @@ import ca.uhn.fhir.jpa.search.builder.sql.GeneratedSql;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryExecutor;
import ca.uhn.fhir.jpa.search.builder.sql.SqlObjectFactory;
import ca.uhn.fhir.jpa.search.builder.tasks.SearchTask;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
@ -126,7 +124,6 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterce
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.util.ThreadPoolUtil;
import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.npm.PackageClient;
@ -138,7 +135,6 @@ import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.context.annotation.Scope;
import org.springframework.core.task.AsyncTaskExecutor;
import org.springframework.core.task.TaskExecutor;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.scheduling.TaskScheduler;
import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
@ -172,7 +168,6 @@ import java.util.Date;
@EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data")
@Import({
BeanPostProcessorConfig.class,
BatchJobsConfig.class,
TermCodeSystemConfig.class,
SearchParamConfig.class,
ValidationSupportConfig.class,
@ -325,11 +320,6 @@ public class JpaConfig {
return retVal;
}
@Bean(name = BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
public TaskExecutor jobLaunchingTaskExecutor() {
return ThreadPoolUtil.newThreadPool(0, 10, "job-launcher-");
}
@Bean
public IResourceReindexingSvc resourceReindexingSvc() {
return new ResourceReindexingSvcImpl();

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
View File

@ -70,8 +70,8 @@ import java.util.concurrent.ConcurrentLinkedQueue;
import java.util.concurrent.TimeUnit;
import java.util.function.Supplier;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

9
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/config/BaseTestMdmConfig.java
View File

@ -1,15 +1,11 @@
package ca.uhn.fhir.jpa.mdm.config;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.dao.JpaMdmLinkImplFactory;
import ca.uhn.fhir.jpa.mdm.helper.MdmLinkHelper;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -43,9 +39,4 @@ public abstract class BaseTestMdmConfig {
MdmLinkHelper mdmLinkHelper() {
return new MdmLinkHelper();
}
@Bean
BatchJobHelper batchJobHelper(JobExplorer theJobExplorer) {
return new BatchJobHelper(theJobExplorer);
}
}

3
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/BaseProviderR4Test.java
View File

@ -10,7 +10,6 @@ import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
import ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.mdm.util.MessageHelper;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -39,8 +38,6 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
@Autowired
private MdmControllerHelper myMdmHelper;
@Autowired
BatchJobHelper myBatchJobHelper;
@Autowired
Batch2JobHelper myBatch2JobHelper;
@Autowired
MessageHelper myMessageHelper;

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu3/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java
View File

@ -13,8 +13,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;

2
hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java
View File

@ -27,7 +27,7 @@ import org.springframework.transaction.annotation.Transactional;
import java.io.IOException;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;

2
hapi-fhir-jpaserver-test-r4/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java
View File

@ -51,7 +51,7 @@ import java.util.Optional;
import java.util.stream.Collectors;
import static ca.uhn.fhir.batch2.config.BaseBatch2Config.CHANNEL_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.BULK_IMPORT_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.importpull.BulkImportPullConfig.BULK_IMPORT_JOB_NAME;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;

3
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeDaoTest.java
View File

@ -10,7 +10,6 @@ import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.util.BundleBuilder;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
@ -34,8 +33,6 @@ import static org.mockito.Mockito.when;
class DeleteExpungeDaoTest extends BaseJpaR4Test {
@Autowired
DaoConfig myDaoConfig;
@Autowired
BatchJobHelper myBatchJobHelper;
@BeforeEach
public void before() {

4
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java
View File

@ -14,8 +14,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.nio.charset.StandardCharsets;
import java.util.List;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
View File

@ -130,7 +130,7 @@ import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.MatcherAssert.assertThat;

3
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java
View File

@ -39,7 +39,6 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizedList;
import ca.uhn.fhir.rest.server.interceptor.auth.SearchNarrowingInterceptor;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.BundleUtil;
@ -119,8 +118,6 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
@Autowired
private DeleteExpungeProvider myDeleteExpungeProvider;
@Autowired
private BatchJobHelper myBatchJobHelper;
@SuppressWarnings("deprecation")
@AfterEach

3
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/StressTestR4Test.java
View File

@ -16,7 +16,6 @@ import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
@ -90,8 +89,6 @@ public class StressTestR4Test extends BaseResourceProviderR4Test {
@Autowired
private DatabaseBackedPagingProvider myPagingProvider;
private int myPreviousMaxPageSize;
@Autowired
private BatchJobHelper myBatchJobHelper;
@Override
@AfterEach

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcTest.java
View File

@ -14,7 +14,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;

11
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincJpaTest.java
View File

@ -5,21 +5,16 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
@Autowired
private BatchJobHelper myBatchJobHelper;
private TermLoaderSvcImpl mySvc;
private ZipCollectionBuilder myFiles;
@ -64,7 +59,8 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
// WIP KHS find equivalent of this in batch2
// myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
@ -90,7 +86,8 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
TermTestUtil.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v268_loincupload.properties");
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
// WIP KHS find equivalent of this in batch2
// myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
View File

@ -51,7 +51,7 @@ import java.util.Properties;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -32,7 +32,7 @@ import java.util.List;
import java.util.Optional;
import java.util.Set;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemDeleteJobTest.java
View File

@ -45,7 +45,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemVersionDeleteJobTest.java
View File

@ -47,7 +47,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;

2
hapi-fhir-jpaserver-test-r5/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5CodeSystemTest.java
View File

@ -11,8 +11,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaDstu3Test.java
View File

@ -32,7 +32,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSubscription;
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.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboStringUniqueDao;
@ -141,9 +140,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
private static IValidationSupport ourJpaValidationSupportChainDstu3;
private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
@Autowired
protected IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
protected ITermDeferredStorageSvc myTerminologyDeferredStorageSvc;
@Autowired

5
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java
View File

@ -35,9 +35,8 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@ -517,8 +516,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Autowired
protected IIdHelperService myIdHelperService;
@Autowired
protected IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
protected ValidationSettings myValidationSettings;
@Autowired
protected IMdmLinkJpaRepository myMdmLinkDao;

20
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaTest.java
View File

@ -75,7 +75,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.test.BaseTest;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.test.utilities.LoggingExtension;
import ca.uhn.fhir.test.utilities.ProxyUtil;
import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
@ -102,10 +101,6 @@ import org.junit.jupiter.api.extension.RegisterExtension;
import org.mockito.Answers;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
import org.springframework.batch.core.repository.dao.JobExecutionDao;
import org.springframework.batch.core.repository.dao.JobInstanceDao;
import org.springframework.batch.core.repository.dao.MapJobExecutionDao;
import org.springframework.batch.core.repository.dao.MapJobInstanceDao;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.orm.jpa.JpaTransactionManager;
@ -202,8 +197,6 @@ public abstract class BaseJpaTest extends BaseTest {
@Autowired(required = false)
protected IFulltextSearchSvc myFulltestSearchSvc;
@Autowired(required = false)
protected BatchJobHelper myBatchJobHelper;
@Autowired(required = false)
protected Batch2JobHelper myBatch2JobHelper;
@Autowired
protected ITermConceptDao myTermConceptDao;
@ -230,24 +223,11 @@ public abstract class BaseJpaTest extends BaseTest {
private IResourceHistoryTableDao myResourceHistoryTableDao;
@Autowired
private IForcedIdDao myForcedIdDao;
@Autowired(required = false)
private JobExecutionDao myMapJobExecutionDao;
@Autowired(required = false)
private JobInstanceDao myMapJobInstanceDao;
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
return ClasspathUtil.loadResource(myFhirContext, type, resourceName);
}
@AfterEach
public void afterEnsureNoStaleBatchJobs() {
if (myMapJobInstanceDao != null) {
myBatchJobHelper.ensureNoRunningJobs();
ProxyUtil.getSingletonTarget(myMapJobExecutionDao, MapJobExecutionDao.class).clear();
ProxyUtil.getSingletonTarget(myMapJobInstanceDao, MapJobInstanceDao.class).clear();
}
}
@AfterEach
public void afterPerformCleanup() {
BaseHapiFhirDao.setDisableIncrementOnUpdateForUnitTest(false);

13
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestJPAConfig.java
View File

@ -37,8 +37,6 @@ import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import ca.uhn.fhir.jpa.test.Batch2JobHelper;
import ca.uhn.fhir.jpa.test.util.StoppableSubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.test.util.SubscriptionTestUtil;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -79,13 +77,9 @@ public class TestJPAConfig {
return config;
}
/*
Please do not rename this bean to "transactionManager()" as this will conflict with the transactionManager
provided by Spring Batch.
*/
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
@ -103,11 +97,6 @@ public class TestJPAConfig {
return new StoppableSubscriptionDeliveringRestHookSubscriber();
}
@Bean
public BatchJobHelper batchJobHelper(JobExplorer theJobExplorer) {
return new BatchJobHelper(theJobExplorer);
}
@Bean
public Batch2JobHelper batch2JobHelper(IJobMaintenanceService theJobMaintenanceService, IJobCoordinator theJobCoordinator, IJobPersistence theJobPersistence) {
return new Batch2JobHelper(theJobMaintenanceService, theJobCoordinator, theJobPersistence);

123
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/job/DynamicJobFlowSandbox.java
View File

@ -1,123 +0,0 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 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 com.google.common.collect.Lists;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.job.builder.FlowBuilder;
import org.springframework.batch.core.job.builder.SimpleJobBuilder;
import org.springframework.batch.core.job.flow.Flow;
import org.springframework.batch.core.job.flow.support.SimpleFlow;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import java.util.List;
import java.util.stream.Collectors;
/**
* Not intended to ever run. Used as a sandbox for "interesting" jobs
*/
public class DynamicJobFlowSandbox {
protected static final Logger ourLog = LoggerFactory.getLogger(DynamicJobFlowSandbox.class);
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Autowired
private StepBuilderFactory myStepBuilderFactory;
private List<Long> versionPidList = Lists.newArrayList(3L, 5L);
@Bean
public Job testJob() {
SimpleJobBuilder jobBuilder = myJobBuilderFactory.get("job")
.start(stepPreFlow());
// add a flow for each Pid
List<Flow> flowForEachPidList = versionPidList.stream().map(this::getFlowForPid).collect(Collectors.toList());
flowForEachPidList.forEach( flowForPid -> jobBuilder.on("COMPLETED").to(flowForPid) );
return jobBuilder.next(stepPostFlow()).build();
}
private Flow getFlowForPid(Long theLong) {
return new FlowBuilder<SimpleFlow>("flow-for-Pid-" + theLong)
.start(flowStep1(theLong))
.next(fllowStep2(theLong))
.build();
}
public Step flowStep1(long theLong) {
String name = "flow-step-1-for-Pid-" + theLong;
return myStepBuilderFactory.get(name)
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\n" + name + " executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
public Step fllowStep2(long theLong) {
String name = "flow-step-2-for-Pid-" + theLong;
return myStepBuilderFactory.get(name)
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\n" + name + " executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
public Step stepPreFlow() {
return myStepBuilderFactory.get("step-pre-flow")
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\nstep-pre-flow executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
public Step stepPostFlow() {
return myStepBuilderFactory.get("step-post-flow")
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\nstep-post-flow executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
}

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

7
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/SchemaInitializationProvider.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.migrate.tasks;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.tasks.api.ISchemaInitializationProvider;
import com.google.common.base.Charsets;
@ -32,6 +32,7 @@ import javax.annotation.Nonnull;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -57,6 +58,10 @@ public class SchemaInitializationProvider implements ISchemaInitializationProvid
@Override
public List<String> getSqlStatements(DriverTypeEnum theDriverType) {
if (!isEnabled()) {
return Collections.emptyList();
}
List<String> retval = new ArrayList<>();
String initScript = mySchemaFileClassPath + "/" + getInitScript(theDriverType);

11
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/Builder.java
View File

@ -92,17 +92,18 @@ public class Builder {
return task;
}
public Builder initializeSchema(String theVersion, ISchemaInitializationProvider theSchemaInitializationProvider) {
mySink.addTask(new InitializeSchemaTask(myRelease, theVersion, theSchemaInitializationProvider));
return this;
public InitializeSchemaTask initializeSchema(String theVersion, ISchemaInitializationProvider theSchemaInitializationProvider) {
InitializeSchemaTask task = new InitializeSchemaTask(myRelease, theVersion, theSchemaInitializationProvider);
mySink.addTask(task);
return task;
}
@SuppressWarnings("unused")
public Builder initializeSchema(String theVersion, String theSchemaName, ISchemaInitializationProvider theSchemaInitializationProvider) {
public InitializeSchemaTask initializeSchema(String theVersion, String theSchemaName, ISchemaInitializationProvider theSchemaInitializationProvider) {
InitializeSchemaTask task = new InitializeSchemaTask(myRelease, theVersion, theSchemaInitializationProvider);
task.setDescription("Initialize " + theSchemaName + " schema");
mySink.addTask(task);
return this;
return task;
}
public Builder executeRawSql(String theVersion, DriverTypeEnum theDriver, @Language("SQL") String theSql) {

4
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/ISchemaInitializationProvider.java
View File

@ -35,4 +35,8 @@ public interface ISchemaInitializationProvider {
ISchemaInitializationProvider setSchemaDescription(String theSchemaDescription);
boolean canInitializeSchema();
default boolean isEnabled() {
return true;
}
}

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

4
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/importpull/BulkImportPullConfig.java
View File

@ -26,7 +26,6 @@ import ca.uhn.fhir.batch2.importpull.models.BulkImportRecord;
import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
@ -34,6 +33,7 @@ import org.springframework.context.annotation.Configuration;
@Configuration
public class BulkImportPullConfig {
public static final String BULK_IMPORT_JOB_NAME = "bulkImportJob";
@Autowired
private FhirContext myFhirContext;
@ -48,7 +48,7 @@ public class BulkImportPullConfig {
public JobDefinition bulkImportPullJobDefinition() {
return JobDefinition
.newBuilder()
.setJobDefinitionId(BatchConstants.BULK_IMPORT_JOB_NAME)
.setJobDefinitionId(BULK_IMPORT_JOB_NAME)
.setJobDescription("Performs bulk import pull job")
.setJobDefinitionVersion(1)
.gatedExecution()

12
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/termcodesystem/TermCodeSystemJobConfig.java
View File

@ -40,11 +40,19 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
@Configuration
public class TermCodeSystemJobConfig {
/**
* TermCodeSystem delete
*/
public static final String TERM_CODE_SYSTEM_DELETE_JOB_NAME = "termCodeSystemDeleteJob";
/**
* TermCodeSystemVersion delete
*/
public static final String TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME = "termCodeSystemVersionDeleteJob";
@Autowired
private ITermCodeSystemDeleteJobSvc myITermCodeSystemSvc;

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.2.0-PRE9-SNAPSHOT</version>
<version>6.2.0-PRE10-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/pid/HomogeneousResourcePidList.java
View File

@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.api.pid;
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import io.micrometer.core.lang.NonNull;
import javax.annotation.Nonnull;
import java.util.Collection;
import java.util.Date;
@ -30,7 +30,7 @@ import java.util.Date;
* A resource pid list where all pids have the same resource type
*/
public class HomogeneousResourcePidList extends BaseResourcePidList {
@NonNull
@Nonnull
final String myResourceType;
public HomogeneousResourcePidList(String theResourceType, Collection<ResourcePersistentId> theIds, Date theLastDate) {

4
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/pid/MixedResourcePidList.java
View File

@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.api.pid;
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import io.micrometer.core.lang.NonNull;
import javax.annotation.Nonnull;
import java.util.Collection;
import java.util.Date;
import java.util.List;
@ -31,7 +31,7 @@ import java.util.List;
* A resource pid list where the pids can have different resource types
*/
public class MixedResourcePidList extends BaseResourcePidList {
@NonNull
@Nonnull
final List<String> myResourceTypes;
public MixedResourcePidList(List<String> theResourceTypes, Collection<ResourcePersistentId> theIds, Date theLastDate) {

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