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hapi-fhir
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Streamline expunge operation

This commit is contained in:
James Agnew 2018-11-15 11:35:50 +01:00
parent 75210d614b
commit 84acafe3af
10 changed files with 64 additions and 19 deletions
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2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -188,7 +188,7 @@
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring4</artifactId>
<artifactId>thymeleaf-spring5</artifactId>
</dependency>
<!-- Dependencies for Schematron -->

2
hapi-fhir-jpaserver-base/pom.xml
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@ -163,7 +163,7 @@
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring4</artifactId>
<artifactId>thymeleaf-spring5</artifactId>
</dependency>
<!-- For UCUM: TODO we should replace this with org.fhir UCUM -->

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
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@ -42,6 +42,7 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.core.env.Environment;
import org.springframework.core.task.AsyncTaskExecutor;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.orm.hibernate5.HibernateExceptionTranslator;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@ -162,7 +163,7 @@ public abstract class BaseConfig implements SchedulingConfigurer {
return new SubscriptionWebsocketInterceptor();
}
@Bean(name = TASK_EXECUTOR_NAME)
@Bean()
public TaskScheduler taskScheduler() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
retVal.setConcurrentExecutor(scheduledExecutorService());
@ -170,6 +171,14 @@ public abstract class BaseConfig implements SchedulingConfigurer {
return retVal;
}
@Bean(name = TASK_EXECUTOR_NAME)
public AsyncTaskExecutor taskExecutor() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
retVal.setConcurrentExecutor(scheduledExecutorService());
retVal.setScheduledExecutor(scheduledExecutorService());
return retVal;
}
@Bean
public IResourceReindexingSvc resourceReindexingSvc() {
return new ResourceReindexingSvcImpl();

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -37,6 +37,7 @@ import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import ca.uhn.fhir.jpa.dao.data.*;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
@ -255,6 +256,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
protected IResourceIndexedSearchParamStringDao myResourceIndexedSearchParamStringDao;
@Autowired()
protected IResourceIndexedSearchParamTokenDao myResourceIndexedSearchParamTokenDao;
@Autowired
protected IResourceLinkDao myResourceLinkDao;
@Autowired()
protected IResourceIndexedSearchParamDateDao myResourceIndexedSearchParamDateDao;
@Autowired()
@ -328,6 +331,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
protected ExpungeOutcome doExpunge(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions) {
TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
ourLog.info("Expunge: ResourceName[{}] Id[{}] Version[{}] Options[{}]", theResourceName, theResourceId, theVersion, theExpungeOptions);
if (!getConfig().isExpungeEnabled()) {
@ -367,11 +371,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
});
/*
* Delete any search result cache entries pointing to the given resource
* Delete any search result cache entries pointing to the given resource. We do
* this in batches to avoid sending giant batches of parameters to the DB
*/
if (resourceIds.getContent().size() > 0) {
List<List<Long>> partitions = Lists.partition(resourceIds.getContent(), 800);
for (List<Long> nextPartition : partitions) {
ourLog.info("Expunging any search results pointing to {} resources", nextPartition.size());
txTemplate.execute(t -> {
mySearchResultDao.deleteByResourceIds(resourceIds.getContent());
mySearchResultDao.deleteByResourceIds(nextPartition);
return null;
});
}
@ -438,7 +445,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
ourLog.info("** BEGINNING GLOBAL $expunge **");
TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
txTemplate.execute(t -> {
doExpungeEverythingQuery("UPDATE " + ResourceHistoryTable.class.getSimpleName() + " d SET d.myForcedId = null");
doExpungeEverythingQuery("UPDATE " + ResourceTable.class.getSimpleName() + " d SET d.myForcedId = null");
@ -521,6 +528,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
myResourceIndexedSearchParamQuantityDao.deleteAll(resource.getParamsQuantity());
myResourceIndexedSearchParamStringDao.deleteAll(resource.getParamsString());
myResourceIndexedSearchParamTokenDao.deleteAll(resource.getParamsToken());
myResourceLinkDao.deleteAll(resource.getResourceLinks());
myResourceLinkDao.deleteAll(resource.getResourceLinksAsTarget());
myResourceTagDao.deleteAll(resource.getTags());
resource.getTags().clear();

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
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@ -65,7 +65,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
@Override
@Transactional(propagation = Propagation.REQUIRED)
@Transactional(propagation = Propagation.NEVER)
public ExpungeOutcome expunge(ExpungeOptions theExpungeOptions) {
return doExpunge(null, null, null, theExpungeOptions);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceLinkDao.java
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@ -25,5 +25,7 @@ import org.springframework.data.jpa.repository.JpaRepository;
import ca.uhn.fhir.jpa.entity.ResourceLink;
public interface IResourceLinkDao extends JpaRepository<ResourceLink, Long> {
// nothing
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
* 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.
@ -185,27 +185,33 @@ public class ResourceTable extends BaseHasResource implements Serializable {
@IndexedEmbedded()
@OptimisticLock(excluded = true)
private Collection<ResourceLink> myResourceLinks;
@OneToMany(mappedBy = "myTargetResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@IndexedEmbedded()
@OptimisticLock(excluded = true)
private Collection<ResourceLink> myResourceLinksAsTarget;
@Column(name = "RES_TYPE", length = RESTYPE_LEN)
@Field
@OptimisticLock(excluded = true)
private String myResourceType;
@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@OptimisticLock(excluded = true)
private Collection<SearchParamPresent> mySearchParamPresents;
@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@OptimisticLock(excluded = true)
private Set<ResourceTag> myTags;
@Transient
private transient boolean myUnchangedInCurrentOperation;
@Version
@Column(name = "RES_VER")
private long myVersion;
public Collection<ResourceLink> getResourceLinksAsTarget() {
if (myResourceLinksAsTarget == null) {
myResourceLinksAsTarget = new ArrayList<>();
}
return myResourceLinksAsTarget;
}
@Override
public ResourceTag addTag(TagDefinition theTag) {
for (ResourceTag next : getTags()) {

2
hapi-fhir-testpage-overlay/pom.xml
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@ -67,7 +67,7 @@
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring4</artifactId>
<artifactId>thymeleaf-spring5</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>

4
pom.xml
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@ -518,9 +518,9 @@
<jsr305_version>3.0.2</jsr305_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.3.6.Final</hibernate_version>
<hibernate_search_version>5.10.3.Final</hibernate_search_version>
<hibernate_validator_version>5.4.1.Final</hibernate_validator_version>
<!-- Update lucene version when you update hibernate-search version -->
<hibernate_search_version>5.10.3.Final</hibernate_search_version>
<httpcore_version>4.4.6</httpcore_version>
<httpclient_version>4.5.3</httpclient_version>
<jackson_version>2.9.7</jackson_version>
@ -1246,7 +1246,7 @@
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring4</artifactId>
<artifactId>thymeleaf-spring5</artifactId>
<version>${thymeleaf-version}</version>
</dependency>
<dependency>

19
src/changes/changes.xml
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@ -6,6 +6,25 @@
<title>HAPI FHIR Changelog</title>
</properties>
<body>
<release version="3.7.0" date="TBD" description="Gale">
<action type="add">
The version of a few dependencies have been bumped to the
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>thymeleaf-spring4 (Testpage Overlay) has been replaced with thymeleaf-spring5</li>
</ul>
]]>
</action>
<action type="fix">
The JPA server $expunge operation could sometimes fail to expunge if
another resource linked to a resource that was being
expunged. This has been corrected. In addition, the $expunge operation
has been refactored to use smaller chunks of work
within a single DB transaction. This improves performance and reduces contention when
performing large expunge workloads.
</action>
</release>
<release version="3.6.0" date="2018-11-12" description="Food">
<action type="add">
The version of a few dependencies have been bumped to the