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hapi-fhir
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Merging master into working branch. 

# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
This commit is contained in:
Diederik Muylwyk 2019-09-09 19:01:29 -04:00
parent dbe5a36f26 95e75d0a7d
commit 67d24eedff
83 changed files with 1634 additions and 1226 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java
View File

@ -182,4 +182,13 @@ public class TestUtil {
return defaultString(theString).replace("\r", "");
}
/**
* <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
* <p>
* Strip \r chars from a string to account for line ending platform differences
*/
public static String stripWhitespace(String theString) {
return stripReturns(theString).replace(" ", "");
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -14,6 +14,10 @@ import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
import ca.uhn.fhir.jpa.subscription.dbmatcher.CompositeInMemoryDaoSubscriptionMatcher;
@ -143,6 +147,16 @@ public abstract class BaseConfig implements SchedulingConfigurer {
return new BinaryStorageInterceptor();
}
@Bean
public ISearchCacheSvc searchCacheSvc() {
return new DatabaseSearchCacheSvcImpl();
}
@Bean
public ISearchResultCacheSvc searchResultCacheSvc() {
return new DatabaseSearchResultCacheSvcImpl();
}
@Bean
public TaskScheduler taskScheduler() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -19,6 +19,8 @@ import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
import ca.uhn.fhir.jpa.searchparam.extractor.LogicalReferenceHelper;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
@ -156,7 +158,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@Autowired
private PlatformTransactionManager myPlatformTransactionManager;
@Autowired
private ISearchDao mySearchDao;
private ISearchCacheSvc mySearchCacheSvc;
@Autowired
private ISearchResultCacheSvc mySearchResultCacheSvc;
@Autowired
private ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
@ -463,7 +467,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
}
search = mySearchDao.save(search);
search = mySearchCacheSvc.save(search);
return new PersistedJpaBundleProvider(theRequest, search.getUuid(), this);
}
@ -489,7 +493,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
theProvider.setContext(getContext());
theProvider.setEntityManager(myEntityManager);
theProvider.setPlatformTransactionManager(myPlatformTransactionManager);
theProvider.setSearchDao(mySearchDao);
theProvider.setSearchCacheSvc(mySearchCacheSvc);
theProvider.setSearchCoordinatorSvc(mySearchCoordinatorSvc);
theProvider.setInterceptorBroadcaster(myInterceptorBroadcaster);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -54,7 +54,6 @@ import ca.uhn.fhir.validation.*;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.r4.model.InstantType;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -72,6 +71,7 @@ import javax.annotation.PostConstruct;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
import javax.servlet.http.HttpServletResponse;
import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.util.*;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDao.java
View File

@ -44,7 +44,10 @@ import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import javax.servlet.http.HttpServletResponse;
import java.util.*;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* Note that this interface is not considered a stable interface. While it is possible to build applications

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirSystemDao.java
View File

@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.util.ExpungeOptions;
import ca.uhn.fhir.jpa.util.ExpungeOutcome;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import com.google.common.annotations.Beta;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ISearchDao.java
View File

@ -10,6 +10,7 @@ import org.springframework.data.repository.query.Param;
import java.util.Collection;
import java.util.Date;
import java.util.Optional;
/*
* #%L
@ -33,15 +34,12 @@ import java.util.Date;
public interface ISearchDao extends JpaRepository<Search, Long> {
@Query("SELECT s FROM Search s WHERE s.myUuid = :uuid")
Search findByUuid(@Param("uuid") String theUuid);
@Query("SELECT s FROM Search s LEFT OUTER JOIN FETCH s.myIncludes WHERE s.myUuid = :uuid")
Optional<Search> findByUuidAndFetchIncludes(@Param("uuid") String theUuid);
@Query("SELECT s.myId FROM Search s WHERE s.mySearchLastReturned < :cutoff")
Slice<Long> findWhereLastReturnedBefore(@Param("cutoff") Date theCutoff, Pageable thePage);
// @SqlQuery("SELECT s FROM Search s WHERE s.myCreated < :cutoff")
// public Collection<Search> findWhereCreatedBefore(@Param("cutoff") Date theCutoff);
@Query("SELECT s FROM Search s WHERE s.myResourceType = :type AND mySearchQueryStringHash = :hash AND s.myCreated > :cutoff AND s.myDeleted = false")
Collection<Search> find(@Param("type") String theResourceType, @Param("hash") int theHashCode, @Param("cutoff") Date theCreatedCutoff);

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ISearchIncludeDao.java
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@ -20,14 +20,13 @@ package ca.uhn.fhir.jpa.dao.data;
* #L%
*/
import ca.uhn.fhir.jpa.entity.SearchInclude;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.entity.SearchInclude;
public interface ISearchIncludeDao extends JpaRepository<SearchInclude, Long> {
public interface ISearchIncludeDao extends JpaRepository<SearchInclude, Long> {
@Modifying
@Query(value="DELETE FROM SearchInclude r WHERE r.mySearchPid = :search")

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ISearchResultDao.java
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@ -1,8 +1,6 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchResult;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
@ -10,9 +8,7 @@ import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
/*
* #%L
@ -34,21 +30,17 @@ import java.util.Set;
* #L%
*/
public interface ISearchResultDao extends JpaRepository<SearchResult, Long> {
public interface ISearchResultDao extends JpaRepository<SearchResult, Long> {
@Query(value="SELECT r.myResourcePid FROM SearchResult r WHERE r.mySearch = :search ORDER BY r.myOrder ASC")
Page<Long> findWithSearchUuid(@Param("search") Search theSearch, Pageable thePage);
@Query(value="SELECT r.myResourcePid FROM SearchResult r WHERE r.mySearchPid = :search ORDER BY r.myOrder ASC")
Slice<Long> findWithSearchPid(@Param("search") Long theSearchPid, Pageable thePage);
@Query(value="SELECT r.myResourcePid FROM SearchResult r WHERE r.mySearch = :search")
List<Long> findWithSearchUuidOrderIndependent(@Param("search") Search theSearch);
@Query(value="SELECT r.myResourcePid FROM SearchResult r WHERE r.mySearchPid = :search")
List<Long> findWithSearchPidOrderIndependent(@Param("search") Long theSearchPid);
@Query(value="SELECT r.myId FROM SearchResult r WHERE r.mySearchPid = :search")
Slice<Long> findForSearch(Pageable thePage, @Param("search") Long theSearchPid);
@Modifying
@Query("DELETE FROM SearchResult s WHERE s.myResourcePid IN :ids")
void deleteByResourceIds(@Param("ids") List<Long> theContent);
@Modifying
@Query("DELETE FROM SearchResult s WHERE s.myId IN :ids")
void deleteByIds(@Param("ids") List<Long> theContent);

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeOperation.java
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@ -84,7 +84,6 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
private void expungeDeletedResources() {
Slice<Long> resourceIds = findHistoricalVersionsOfDeletedResources();
deleteSearchResultCacheEntries(resourceIds);
deleteHistoricalVersions(resourceIds);
if (expungeLimitReached()) {
return;
@ -123,10 +122,6 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
myPartitionRunner.runInPartitionedThreads(theResourceIds, partition -> myExpungeDaoService.expungeHistoricalVersionsOfIds(myRequestDetails, partition, myRemainingCount));
}
private void deleteSearchResultCacheEntries(Slice<Long> theResourceIds) {
myPartitionRunner.runInPartitionedThreads(theResourceIds, partition -> myExpungeDaoService.deleteByResourceIdPartitions(partition));
}
private ExpungeOutcome expungeOutcome() {
return new ExpungeOutcome().setDeletedCount(myExpungeOptions.getLimit() - myRemainingCount.get());
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/IResourceExpungeService.java
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@ -37,7 +37,5 @@ public interface IResourceExpungeService {
void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<Long> thePartition, AtomicInteger theRemainingCount);
void deleteByResourceIdPartitions(List<Long> thePartition);
void deleteAllSearchParams(Long theResourceId);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
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@ -58,8 +58,6 @@ class ResourceExpungeService implements IResourceExpungeService {
@Autowired
private IResourceTableDao myResourceTableDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Autowired
private IResourceHistoryTableDao myResourceHistoryTableDao;
@Autowired
private IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao;
@ -250,12 +248,6 @@ class ResourceExpungeService implements IResourceExpungeService {
}
}
@Override
@Transactional
public void deleteByResourceIdPartitions(List<Long> theResourceIds) {
mySearchResultDao.deleteByResourceIds(theResourceIds);
}
private Slice<Long> toSlice(ResourceHistoryTable myVersion) {
Validate.notNull(myVersion);
return new SliceImpl<>(Collections.singletonList(myVersion.getId()));

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

@ -1,10 +1,10 @@
package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
import org.apache.commons.lang3.SerializationUtils;
import org.hibernate.annotations.OptimisticLock;
@ -80,8 +80,6 @@ public class Search implements ICachedSearchDetails, Serializable {
private Long myResourceId;
@Column(name = "RESOURCE_TYPE", length = 200, nullable = true)
private String myResourceType;
@OneToMany(mappedBy = "mySearch", fetch = FetchType.LAZY)
private Collection<SearchResult> myResults;
@NotNull
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "SEARCH_LAST_RETURNED", nullable = false, updatable = false)

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SearchResult.java
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@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder;
import javax.persistence.*;
@ -39,17 +39,11 @@ public class SearchResult implements Serializable {
@Id
@Column(name = "PID")
private Long myId;
@Column(name = "SEARCH_ORDER", nullable = false)
@Column(name = "SEARCH_ORDER", nullable = false, insertable = true, updatable = false)
private int myOrder;
@ManyToOne
@JoinColumn(name = "RESOURCE_PID", referencedColumnName = "RES_ID", foreignKey = @ForeignKey(name = "FK_SEARCHRES_RES"), insertable = false, updatable = false, nullable = false)
private ResourceTable myResource;
@Column(name = "RESOURCE_PID", insertable = true, updatable = false, nullable = false)
private Long myResourcePid;
@ManyToOne
@JoinColumn(name = "SEARCH_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_SEARCHRES_SEARCH"))
private Search mySearch;
@Column(name = "SEARCH_PID", insertable = false, updatable = false, nullable = false)
@Column(name = "SEARCH_PID", insertable = true, updatable = false, nullable = false)
private Long mySearchPid;
/**
@ -63,7 +57,8 @@ public class SearchResult implements Serializable {
* Constructor
*/
public SearchResult(Search theSearch) {
mySearch = theSearch;
Validate.notNull(theSearch.getId());
mySearchPid = theSearch.getId();
}
@Override

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
View File

@ -31,12 +31,10 @@ import java.util.Collection;
import static org.apache.commons.lang3.StringUtils.length;
//@formatter:off
@Table(name = "TRM_CODESYSTEM_VER"
// Note, we used to have a constraint named IDX_CSV_RESOURCEPID_AND_VER (don't reuse this)
)
@Entity()
//@formatter:on
public class TermCodeSystemVersion implements Serializable {
private static final long serialVersionUID = 1L;

0
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/.editorconfig
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38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
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@ -26,11 +26,11 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.IDao;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.server.*;
@ -46,7 +46,6 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
@ -64,7 +63,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
private EntityManager myEntityManager;
private PlatformTransactionManager myPlatformTransactionManager;
private ISearchCoordinatorSvc mySearchCoordinatorSvc;
private ISearchDao mySearchDao;
private ISearchCacheSvc mySearchCacheSvc;
private Search mySearchEntity;
private String myUuid;
private boolean myCacheHit;
@ -192,27 +191,16 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
if (mySearchEntity == null) {
ensureDependenciesInjected();
TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
txTemplate.setIsolationLevel(TransactionDefinition.ISOLATION_READ_COMMITTED);
return txTemplate.execute(s -> {
try {
setSearchEntity(mySearchDao.findByUuid(myUuid));
Optional<Search> search = mySearchCacheSvc.fetchByUuid(myUuid);
if (!search.isPresent()) {
return false;
}
if (mySearchEntity == null) {
return false;
}
setSearchEntity(search.get());
ourLog.trace("Retrieved search with version {} and total {}", mySearchEntity.getVersion(), mySearchEntity.getTotalCount());
ourLog.trace("Retrieved search with version {} and total {}", mySearchEntity.getVersion(), mySearchEntity.getTotalCount());
// Load the includes now so that they are available outside of this transaction
mySearchEntity.getIncludes().size();
return true;
} catch (NoResultException e) {
return false;
}
});
return true;
}
return true;
}
@ -292,10 +280,6 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
mySearchCoordinatorSvc = theSearchCoordinatorSvc;
}
public void setSearchDao(ISearchDao theSearchDao) {
mySearchDao = theSearchDao;
}
// Note: Leave as protected, HSPC depends on this
@SuppressWarnings("WeakerAccess")
protected void setSearchEntity(Search theSearchEntity) {
@ -353,4 +337,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
public void setInterceptorBroadcaster(IInterceptorBroadcaster theInterceptorBroadcaster) {
myInterceptorBroadcaster = theInterceptorBroadcaster;
}
public void setSearchCacheSvc(ISearchCacheSvc theSearchCacheSvc) {
mySearchCacheSvc = theSearchCacheSvc;
}
}

464
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -25,16 +25,14 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.entity.SearchResult;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.model.api.Include;
@ -56,15 +54,12 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.AbstractPageRequest;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Sort;
import org.springframework.orm.jpa.JpaDialect;
@ -83,7 +78,10 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.time.Instant;
import java.time.temporal.ChronoUnit;
import java.util.*;
import java.util.concurrent.*;
@ -106,16 +104,14 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
private long myMaxMillisToWaitForRemoteResults = DateUtils.MILLIS_PER_MINUTE;
private boolean myNeverUseLocalSearchForUnitTests;
@Autowired
private ISearchDao mySearchDao;
@Autowired
private ISearchIncludeDao mySearchIncludeDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Autowired
private IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
private PlatformTransactionManager myManagedTxManager;
@Autowired
private ISearchCacheSvc mySearchCacheSvc;
@Autowired
private ISearchResultCacheSvc mySearchResultCacheSvc;
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private IPagingProvider myPagingProvider;
@ -134,6 +130,12 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
myExecutor = Executors.newCachedThreadPool(threadFactory);
}
@VisibleForTesting
public void setSearchCacheServicesForUnitTest(ISearchCacheSvc theSearchCacheSvc, ISearchResultCacheSvc theSearchResultCacheSvc) {
mySearchCacheSvc = theSearchCacheSvc;
mySearchResultCacheSvc = theSearchResultCacheSvc;
}
@PostConstruct
public void start() {
if (myManagedTxManager instanceof JpaTransactionManager) {
@ -184,13 +186,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
search = txTemplate.execute(t -> mySearchDao.findByUuid(theUuid));
if (search == null) {
ourLog.debug("Client requested unknown paging ID[{}]", theUuid);
String msg = myContext.getLocalizer().getMessage(PageMethodBinding.class, "unknownSearchId", theUuid);
throw new ResourceGoneException(msg);
}
search = mySearchCacheSvc
.fetchByUuid(theUuid)
.orElseThrow(() -> {
ourLog.debug("Client requested unknown paging ID[{}]", theUuid);
String msg = myContext.getLocalizer().getMessage(PageMethodBinding.class, "unknownSearchId", theUuid);
return new ResourceGoneException(msg);
});
verifySearchHasntFailedOrThrowInternalErrorException(search);
if (search.getStatus() == SearchStatusEnum.FINISHED) {
@ -210,7 +212,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
// If the search was saved in "pass complete mode" it's probably time to
// start a new pass
if (search.getStatus() == SearchStatusEnum.PASSCMPLET) {
Optional<Search> newSearch = tryToMarkSearchAsInProgress(search);
Optional<Search> newSearch = mySearchCacheSvc.tryToMarkSearchAsInProgress(search);
if (newSearch.isPresent()) {
search = newSearch.get();
String resourceType = search.getResourceType();
@ -229,60 +231,22 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
final Pageable page = toPage(theFrom, theTo);
if (page == null) {
return Collections.emptyList();
}
final Search foundSearch = search;
ourLog.trace("Loading stored search");
List<Long> retVal = txTemplate.execute(theStatus -> {
final List<Long> resultPids = new ArrayList<>();
Page<Long> searchResultPids = mySearchResultDao.findWithSearchUuid(foundSearch, page);
for (Long next : searchResultPids) {
resultPids.add(next);
}
return resultPids;
});
return retVal;
return mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
}
private Optional<Search> tryToMarkSearchAsInProgress(Search theSearch) {
ourLog.trace("Going to try to change search status from {} to {}", theSearch.getStatus(), SearchStatusEnum.LOADING);
try {
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
txTemplate.afterPropertiesSet();
return txTemplate.execute(t -> {
Search search = mySearchDao.findById(theSearch.getId()).orElse(theSearch);
if (search.getStatus() != SearchStatusEnum.PASSCMPLET) {
throw new IllegalStateException("Can't change to LOADING because state is " + theSearch.getStatus());
}
search.setStatus(SearchStatusEnum.LOADING);
Search newSearch = mySearchDao.save(search);
return Optional.of(newSearch);
});
} catch (Exception e) {
ourLog.warn("Failed to activate search: {}", e.toString());
ourLog.trace("Failed to activate search", e);
return Optional.empty();
}
}
private void populateBundleProvider(PersistedJpaBundleProvider theRetVal) {
theRetVal.setContext(myContext);
theRetVal.setEntityManager(myEntityManager);
theRetVal.setPlatformTransactionManager(myManagedTxManager);
theRetVal.setSearchDao(mySearchDao);
theRetVal.setSearchCacheSvc(mySearchCacheSvc);
theRetVal.setSearchCoordinatorSvc(this);
theRetVal.setInterceptorBroadcaster(myInterceptorBroadcaster);
}
@Override
public IBundleProvider registerSearch(final IDao theCallingDao, final SearchParameterMap theParams, String theResourceType, CacheControlDirective theCacheControlDirective, RequestDetails theRequestDetails) {
StopWatch w = new StopWatch();
final String searchUuid = UUID.randomUUID().toString();
ourLog.debug("Registering new search {}", searchUuid);
@ -292,6 +256,185 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
sb.setType(resourceTypeClass, theResourceType);
sb.setFetchSize(mySyncSize);
final Integer loadSynchronousUpTo = getLoadSynchronousUpToOrNull(theCacheControlDirective);
if (theParams.isLoadSynchronous() || loadSynchronousUpTo != null) {
ourLog.debug("Search {} is loading in synchronous mode", searchUuid);
return executeQuery(theParams, theRequestDetails, searchUuid, sb, loadSynchronousUpTo);
}
/*
* See if there are any cached searches whose results we can return
* instead
*/
boolean useCache = true;
if (theCacheControlDirective != null && theCacheControlDirective.isNoCache() == true) {
useCache = false;
}
final String queryString = theParams.toNormalizedQueryString(myContext);
if (theParams.getEverythingMode() == null) {
if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null && useCache) {
IBundleProvider foundSearchProvider = findCachedQuery(theCallingDao, theParams, theResourceType, theRequestDetails, queryString);
if (foundSearchProvider != null) {
return foundSearchProvider;
}
}
}
return submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, searchUuid, sb, queryString);
}
@NotNull
private IBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString) {
StopWatch w = new StopWatch();
Search search = new Search();
populateSearchEntity(theParams, theResourceType, theSearchUuid, theQueryString, search);
// Interceptor call: STORAGE_PRESEARCH_REGISTERED
HookParams params = new HookParams()
.add(ICachedSearchDetails.class, search)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
SearchTask task = new SearchTask(search, theCallingDao, theParams, theResourceType, theRequestDetails);
myIdToSearchTask.put(search.getUuid(), task);
myExecutor.submit(task);
PersistedJpaSearchFirstPageBundleProvider retVal = new PersistedJpaSearchFirstPageBundleProvider(search, theCallingDao, task, theSb, myManagedTxManager, theRequestDetails);
populateBundleProvider(retVal);
ourLog.debug("Search initial phase completed in {}ms", w.getMillis());
return retVal;
}
@org.jetbrains.annotations.Nullable
private IBundleProvider findCachedQuery(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theQueryString) {
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
PersistedJpaBundleProvider foundSearchProvider = txTemplate.execute(t -> {
// Interceptor call: STORAGE_PRECHECK_FOR_CACHED_SEARCH
HookParams params = new HookParams()
.add(SearchParameterMap.class, theParams)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
Object outcome = JpaInterceptorBroadcaster.doCallHooksAndReturnObject(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRECHECK_FOR_CACHED_SEARCH, params);
if (Boolean.FALSE.equals(outcome)) {
return null;
}
// Check for a search matching the given hash
Search searchToUse = findSearchToUseOrNull(theQueryString, theResourceType);
if (searchToUse == null) {
return null;
}
ourLog.debug("Reusing search {} from cache", searchToUse.getUuid());
// Interceptor call: JPA_PERFTRACE_SEARCH_REUSING_CACHED
params = new HookParams()
.add(SearchParameterMap.class, theParams)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_SEARCH_REUSING_CACHED, params);
mySearchCacheSvc.updateSearchLastReturned(searchToUse, new Date());
PersistedJpaBundleProvider retVal = new PersistedJpaBundleProvider(theRequestDetails, searchToUse.getUuid(), theCallingDao);
retVal.setCacheHit(true);
populateBundleProvider(retVal);
return retVal;
});
if (foundSearchProvider != null) {
return foundSearchProvider;
}
return null;
}
@Nullable
private Search findSearchToUseOrNull(String theQueryString, String theResourceType) {
Search searchToUse = null;
// createdCutoff is in recent past
final Instant createdCutoff = Instant.now().minus(myDaoConfig.getReuseCachedSearchResultsForMillis(), ChronoUnit.MILLIS);
Collection<Search> candidates = mySearchCacheSvc.findCandidatesForReuse(theResourceType, theQueryString, theQueryString.hashCode(), Date.from(createdCutoff));
for (Search nextCandidateSearch : candidates) {
// We should only reuse our search if it was created within the permitted window
// Date.after() is unreliable. Instant.isAfter() always works.
if (theQueryString.equals(nextCandidateSearch.getSearchQueryString()) && nextCandidateSearch.getCreated().toInstant().isAfter(createdCutoff)) {
searchToUse = nextCandidateSearch;
break;
}
}
return searchToUse;
}
private IBundleProvider executeQuery(SearchParameterMap theParams, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, Integer theLoadSynchronousUpTo) {
SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequestDetails, theSearchUuid);
searchRuntimeDetails.setLoadSynchronous(true);
// Execute the query and make sure we return distinct results
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
return txTemplate.execute(t -> {
// Load the results synchronously
final List<Long> pids = new ArrayList<>();
try (IResultIterator resultIter = theSb.createQuery(theParams, searchRuntimeDetails, theRequestDetails)) {
while (resultIter.hasNext()) {
pids.add(resultIter.next());
if (theLoadSynchronousUpTo != null && pids.size() >= theLoadSynchronousUpTo) {
break;
}
if (theParams.getLoadSynchronousUpTo() != null && pids.size() >= theParams.getLoadSynchronousUpTo()) {
break;
}
}
} catch (IOException e) {
ourLog.error("IO failure during database access", e);
throw new InternalErrorException(e);
}
JpaPreResourceAccessDetails accessDetails = new JpaPreResourceAccessDetails(pids, () -> theSb);
HookParams params = new HookParams()
.add(IPreResourceAccessDetails.class, accessDetails)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PREACCESS_RESOURCES, params);
for (int i = pids.size() - 1; i >= 0; i--) {
if (accessDetails.isDontReturnResourceAtIndex(i)) {
pids.remove(i);
}
}
/*
* For synchronous queries, we load all the includes right away
* since we're returning a static bundle with all the results
* pre-loaded. This is ok because syncronous requests are not
* expected to be paged
*
* On the other hand for async queries we load includes/revincludes
* individually for pages as we return them to clients
*/
final Set<Long> includedPids = new HashSet<>();
includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
includedPids.addAll(theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
List<Long> includedPidsList = new ArrayList<>(includedPids);
List<IBaseResource> resources = new ArrayList<>();
theSb.loadResourcesByPid(pids, includedPidsList, resources, false, theRequestDetails);
return new SimpleBundleProvider(resources);
});
}
@org.jetbrains.annotations.Nullable
private Integer getLoadSynchronousUpToOrNull(CacheControlDirective theCacheControlDirective) {
final Integer loadSynchronousUpTo;
if (theCacheControlDirective != null && theCacheControlDirective.isNoStore()) {
if (theCacheControlDirective.getMaxResults() != null) {
@ -305,158 +448,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
} else {
loadSynchronousUpTo = null;
}
if (theParams.isLoadSynchronous() || loadSynchronousUpTo != null) {
ourLog.debug("Search {} is loading in synchronous mode", searchUuid);
SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequestDetails, searchUuid);
searchRuntimeDetails.setLoadSynchronous(true);
// Execute the query and make sure we return distinct results
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
return txTemplate.execute(t -> {
// Load the results synchronously
final List<Long> pids = new ArrayList<>();
try (IResultIterator resultIter = sb.createQuery(theParams, searchRuntimeDetails, theRequestDetails)) {
while (resultIter.hasNext()) {
pids.add(resultIter.next());
if (loadSynchronousUpTo != null && pids.size() >= loadSynchronousUpTo) {
break;
}
if (theParams.getLoadSynchronousUpTo() != null && pids.size() >= theParams.getLoadSynchronousUpTo()) {
break;
}
}
} catch (IOException e) {
ourLog.error("IO failure during database access", e);
throw new InternalErrorException(e);
}
JpaPreResourceAccessDetails accessDetails = new JpaPreResourceAccessDetails(pids, () -> sb);
HookParams params = new HookParams()
.add(IPreResourceAccessDetails.class, accessDetails)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PREACCESS_RESOURCES, params);
for (int i = pids.size() - 1; i >= 0; i--) {
if (accessDetails.isDontReturnResourceAtIndex(i)) {
pids.remove(i);
}
}
/*
* For synchronous queries, we load all the includes right away
* since we're returning a static bundle with all the results
* pre-loaded. This is ok because syncronous requests are not
* expected to be paged
*
* On the other hand for async queries we load includes/revincludes
* individually for pages as we return them to clients
*/
final Set<Long> includedPids = new HashSet<>();
includedPids.addAll(sb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
includedPids.addAll(sb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails));
List<Long> includedPidsList = new ArrayList<>(includedPids);
List<IBaseResource> resources = new ArrayList<>();
sb.loadResourcesByPid(pids, includedPidsList, resources, false, theRequestDetails);
return new SimpleBundleProvider(resources);
});
}
/*
* See if there are any cached searches whose results we can return
* instead
*/
boolean useCache = true;
if (theCacheControlDirective != null && theCacheControlDirective.isNoCache() == true) {
useCache = false;
}
final String queryString = theParams.toNormalizedQueryString(myContext);
if (theParams.getEverythingMode() == null) {
if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null && useCache) {
final Date createdCutoff = new Date(System.currentTimeMillis() - myDaoConfig.getReuseCachedSearchResultsForMillis());
final String resourceType = theResourceType;
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
PersistedJpaBundleProvider foundSearchProvider = txTemplate.execute(t -> {
Search searchToUse = null;
// Interceptor call: STORAGE_PRECHECK_FOR_CACHED_SEARCH
HookParams params = new HookParams()
.add(SearchParameterMap.class, theParams)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
Object outcome = JpaInterceptorBroadcaster.doCallHooksAndReturnObject(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRECHECK_FOR_CACHED_SEARCH, params);
if (Boolean.FALSE.equals(outcome)) {
return null;
}
// Check for a search matching the given hash
int hashCode = queryString.hashCode();
Collection<Search> candidates = mySearchDao.find(resourceType, hashCode, createdCutoff);
for (Search nextCandidateSearch : candidates) {
if (queryString.equals(nextCandidateSearch.getSearchQueryString())) {
searchToUse = nextCandidateSearch;
break;
}
}
PersistedJpaBundleProvider retVal = null;
if (searchToUse != null) {
ourLog.debug("Reusing search {} from cache", searchToUse.getUuid());
// Interceptor call: JPA_PERFTRACE_SEARCH_REUSING_CACHED
params = new HookParams()
.add(SearchParameterMap.class, theParams)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_SEARCH_REUSING_CACHED, params);
searchToUse.setSearchLastReturned(new Date());
mySearchDao.updateSearchLastReturned(searchToUse.getId(), new Date());
retVal = new PersistedJpaBundleProvider(theRequestDetails, searchToUse.getUuid(), theCallingDao);
retVal.setCacheHit(true);
populateBundleProvider(retVal);
}
return retVal;
});
if (foundSearchProvider != null) {
return foundSearchProvider;
}
}
}
Search search = new Search();
populateSearchEntity(theParams, theResourceType, searchUuid, queryString, search);
// Interceptor call: STORAGE_PRESEARCH_REGISTERED
HookParams params = new HookParams()
.add(ICachedSearchDetails.class, search)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
SearchTask task = new SearchTask(search, theCallingDao, theParams, theResourceType, theRequestDetails);
myIdToSearchTask.put(search.getUuid(), task);
myExecutor.submit(task);
PersistedJpaSearchFirstPageBundleProvider retVal = new PersistedJpaSearchFirstPageBundleProvider(search, theCallingDao, task, sb, myManagedTxManager, theRequestDetails);
populateBundleProvider(retVal);
ourLog.debug("Search initial phase completed in {}ms", w.getMillis());
return retVal;
return loadSynchronousUpTo;
}
private void callInterceptorStoragePreAccessResources(IInterceptorBroadcaster theInterceptorBroadcaster, RequestDetails theRequestDetails, ISearchBuilder theSb, List<Long> thePids) {
@ -500,21 +492,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
myNeverUseLocalSearchForUnitTests = theNeverUseLocalSearchForUnitTests;
}
@VisibleForTesting
void setSearchDaoForUnitTest(ISearchDao theSearchDao) {
mySearchDao = theSearchDao;
}
@VisibleForTesting
void setSearchDaoIncludeForUnitTest(ISearchIncludeDao theSearchIncludeDao) {
mySearchIncludeDao = theSearchIncludeDao;
}
@VisibleForTesting
void setSearchDaoResultForUnitTest(ISearchResultDao theSearchResultDao) {
mySearchResultDao = theSearchResultDao;
}
@VisibleForTesting
public void setSyncSizeForUnitTests(int theSyncSize) {
mySyncSize = theSyncSize;
@ -696,20 +673,10 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
List<SearchResult> resultsToSave = Lists.newArrayList();
for (Long nextPid : unsyncedPids) {
SearchResult nextResult = new SearchResult(mySearch);
nextResult.setResourcePid(nextPid);
nextResult.setOrder(myCountSavedTotal);
resultsToSave.add(nextResult);
int order = nextResult.getOrder();
ourLog.trace("Saving ORDER[{}] Resource {}", order, nextResult.getResourcePid());
myCountSavedTotal++;
myCountSavedThisPass++;
}
mySearchResultDao.saveAll(resultsToSave);
// Actually store the results in the query cache storage
myCountSavedTotal += unsyncedPids.size();
myCountSavedThisPass += unsyncedPids.size();
mySearchResultCacheSvc.storeResults(mySearch, mySyncedPids, unsyncedPids);
synchronized (mySyncedPids) {
int numSyncedThisPass = unsyncedPids.size();
@ -877,15 +844,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
private void doSaveSearch() {
Search newSearch;
if (mySearch.getId() == null) {
newSearch = mySearchDao.save(mySearch);
for (SearchInclude next : mySearch.getIncludes()) {
mySearchIncludeDao.save(next);
}
} else {
newSearch = mySearchDao.save(mySearch);
}
Search newSearch = mySearchCacheSvc.save(mySearch);
// mySearchDao.save is not supposed to return null, but in unit tests
// it can if the mock search dao isn't set up to handle that
@ -928,7 +887,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
mySearch.setStatus(SearchStatusEnum.FINISHED);
}
doSaveSearch();
mySearchDao.flush();
}
});
if (wantOnlyCount) {
@ -1058,7 +1016,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
txTemplate.afterPropertiesSet();
txTemplate.execute(t -> {
List<Long> previouslyAddedResourcePids = mySearchResultDao.findWithSearchUuidOrderIndependent(getSearch());
List<Long> previouslyAddedResourcePids = mySearchResultCacheSvc.fetchAllResultPids(getSearch());
ourLog.debug("Have {} previously added IDs in search: {}", previouslyAddedResourcePids.size(), getSearch().getUuid());
setPreviouslyAddedResourcePids(previouslyAddedResourcePids);
return null;

145
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java
View File

@ -21,24 +21,13 @@ package ca.uhn.fhir.jpa.search;
*/
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.model.InstantType;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate;
import java.util.Date;
import java.util.List;
import static ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl.DEFAULT_CUTOFF_SLACK;
/**
* Deletes old searches
@ -49,111 +38,16 @@ import java.util.List;
// in Smile.
//
public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
public static final long DEFAULT_CUTOFF_SLACK = 10 * DateUtils.MILLIS_PER_SECOND;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StaleSearchDeletingSvcImpl.class);
/*
* Be careful increasing this number! We use the number of params here in a
* DELETE FROM foo WHERE params IN (aaaa)
* type query and this can fail if we have 1000s of params
*/
public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT = 500;
public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS = 20000;
private static int ourMaximumResultsToDeleteInOneStatement = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT;
private static int ourMaximumResultsToDeleteInOnePass = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS;
private static Long ourNowForUnitTests;
/*
* We give a bit of extra leeway just to avoid race conditions where a query result
* is being reused (because a new client request came in with the same params) right before
* the result is to be deleted
*/
private long myCutoffSlack = DEFAULT_CUTOFF_SLACK;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private ISearchDao mySearchDao;
@Autowired
private ISearchIncludeDao mySearchIncludeDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Autowired
private PlatformTransactionManager myTransactionManager;
private void deleteSearch(final Long theSearchPid) {
mySearchDao.findById(theSearchPid).ifPresent(searchToDelete -> {
mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
/*
* Note, we're only deleting up to 500 results in an individual search here. This
* is to prevent really long running transactions in cases where there are
* huge searches with tons of results in them. By the time we've gotten here
* we have marked the parent Search entity as deleted, so it's not such a
* huge deal to be only partially deleting search results. They'll get deleted
* eventually
*/
int max = ourMaximumResultsToDeleteInOnePass;
Slice<Long> resultPids = mySearchResultDao.findForSearch(PageRequest.of(0, max), searchToDelete.getId());
if (resultPids.hasContent()) {
List<List<Long>> partitions = Lists.partition(resultPids.getContent(), ourMaximumResultsToDeleteInOneStatement);
for (List<Long> nextPartition : partitions) {
mySearchResultDao.deleteByIds(nextPartition);
}
}
// Only delete if we don't have results left in this search
if (resultPids.getNumberOfElements() < max) {
ourLog.debug("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), new InstantType(searchToDelete.getCreated()), new InstantType(searchToDelete.getSearchLastReturned()));
mySearchDao.deleteByPid(searchToDelete.getId());
} else {
ourLog.debug("Purged {} search results for deleted search {}/{}", resultPids.getSize(), searchToDelete.getId(), searchToDelete.getUuid());
}
});
}
private ISearchCacheSvc mySearchCacheSvc;
@Override
@Transactional(propagation = Propagation.NEVER)
public void pollForStaleSearchesAndDeleteThem() {
if (!myDaoConfig.isExpireSearchResults()) {
return;
}
long cutoffMillis = myDaoConfig.getExpireSearchResultsAfterMillis();
if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null) {
cutoffMillis = Math.max(cutoffMillis, myDaoConfig.getReuseCachedSearchResultsForMillis());
}
final Date cutoff = new Date((now() - cutoffMillis) - myCutoffSlack);
if (ourNowForUnitTests != null) {
ourLog.info("Searching for searches which are before {} - now is {}", new InstantType(cutoff), new InstantType(new Date(now())));
}
ourLog.debug("Searching for searches which are before {}", cutoff);
TransactionTemplate tt = new TransactionTemplate(myTransactionManager);
final Slice<Long> toDelete = tt.execute(theStatus ->
mySearchDao.findWhereLastReturnedBefore(cutoff, PageRequest.of(0, 2000))
);
for (final Long nextSearchToDelete : toDelete) {
ourLog.debug("Deleting search with PID {}", nextSearchToDelete);
tt.execute(t -> {
mySearchDao.updateDeleted(nextSearchToDelete, true);
return null;
});
tt.execute(t -> {
deleteSearch(nextSearchToDelete);
return null;
});
}
int count = toDelete.getContent().size();
if (count > 0) {
if (ourLog.isDebugEnabled()) {
long total = tt.execute(t -> mySearchDao.count());
ourLog.debug("Deleted {} searches, {} remaining", count, total);
}
}
mySearchCacheSvc.pollForStaleSearchesAndDeleteThem();
}
@Scheduled(fixedDelay = DEFAULT_CUTOFF_SLACK)
@ -164,35 +58,4 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
pollForStaleSearchesAndDeleteThem();
}
}
@VisibleForTesting
public void setCutoffSlackForUnitTest(long theCutoffSlack) {
myCutoffSlack = theCutoffSlack;
}
@VisibleForTesting
public static void setMaximumResultsToDeleteInOnePassForUnitTest(int theMaximumResultsToDeleteInOnePass) {
ourMaximumResultsToDeleteInOnePass = theMaximumResultsToDeleteInOnePass;
}
@VisibleForTesting
public static void setMaximumResultsToDeleteForUnitTest(int theMaximumResultsToDelete) {
ourMaximumResultsToDeleteInOneStatement = theMaximumResultsToDelete;
}
private static long now() {
if (ourNowForUnitTests != null) {
return ourNowForUnitTests;
}
return System.currentTimeMillis();
}
/**
* This is for unit tests only, do not call otherwise
*/
@VisibleForTesting
public static void setNowForUnitTests(Long theNowForUnitTests) {
ourNowForUnitTests = theNowForUnitTests;
}
}

64
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/BaseSearchCacheSvcImpl.java vendored Normal file
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@ -0,0 +1,64 @@
package ca.uhn.fhir.jpa.search.cache;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.entity.Search;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
import java.util.Date;
import java.util.Iterator;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
public abstract class BaseSearchCacheSvcImpl implements ISearchCacheSvc {
@Autowired
private PlatformTransactionManager myTxManager;
private ConcurrentHashMap<Long, Date> myUnsyncedLastUpdated = new ConcurrentHashMap<>();
@Override
public void updateSearchLastReturned(Search theSearch, Date theDate) {
myUnsyncedLastUpdated.put(theSearch.getId(), theDate);
}
@Override
@Scheduled(fixedDelay = 10 * DateUtils.MILLIS_PER_SECOND)
public void flushLastUpdated() {
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.execute(t->{
for (Iterator<Map.Entry<Long, Date>> iter = myUnsyncedLastUpdated.entrySet().iterator(); iter.hasNext(); ) {
Map.Entry<Long, Date> next = iter.next();
flushLastUpdated(next.getKey(), next.getValue());
iter.remove();
}
return null;
});
}
protected abstract void flushLastUpdated(Long theSearchId, Date theLastUpdated);
}

261
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchCacheSvcImpl.java vendored Normal file
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@ -0,0 +1,261 @@
package ca.uhn.fhir.jpa.search.cache;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.model.InstantType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionTemplate;
import javax.transaction.Transactional;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Optional;
public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
private static final Logger ourLog = LoggerFactory.getLogger(DatabaseSearchCacheSvcImpl.class);
/*
* Be careful increasing this number! We use the number of params here in a
* DELETE FROM foo WHERE params IN (aaaa)
* type query and this can fail if we have 1000s of params
*/
public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT = 500;
public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS = 20000;
public static final long DEFAULT_CUTOFF_SLACK = 10 * DateUtils.MILLIS_PER_SECOND;
private static int ourMaximumResultsToDeleteInOneStatement = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT;
private static int ourMaximumResultsToDeleteInOnePass = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS;
private static Long ourNowForUnitTests;
/*
* We give a bit of extra leeway just to avoid race conditions where a query result
* is being reused (because a new client request came in with the same params) right before
* the result is to be deleted
*/
private long myCutoffSlack = DEFAULT_CUTOFF_SLACK;
@Autowired
private ISearchDao mySearchDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Autowired
private ISearchIncludeDao mySearchIncludeDao;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private DaoConfig myDaoConfig;
@VisibleForTesting
public void setCutoffSlackForUnitTest(long theCutoffSlack) {
myCutoffSlack = theCutoffSlack;
}
@Transactional(Transactional.TxType.REQUIRED)
@Override
public Search save(Search theSearch) {
Search newSearch;
if (theSearch.getId() == null) {
newSearch = mySearchDao.save(theSearch);
for (SearchInclude next : theSearch.getIncludes()) {
mySearchIncludeDao.save(next);
}
} else {
newSearch = mySearchDao.save(theSearch);
}
return newSearch;
}
@Override
@Transactional(Transactional.TxType.REQUIRED)
public Optional<Search> fetchByUuid(String theUuid) {
Validate.notBlank(theUuid);
return mySearchDao.findByUuidAndFetchIncludes(theUuid);
}
@Override
@Transactional(Transactional.TxType.NEVER)
public Optional<Search> tryToMarkSearchAsInProgress(Search theSearch) {
ourLog.trace("Going to try to change search status from {} to {}", theSearch.getStatus(), SearchStatusEnum.LOADING);
try {
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
txTemplate.afterPropertiesSet();
return txTemplate.execute(t -> {
Search search = mySearchDao.findById(theSearch.getId()).orElse(theSearch);
if (search.getStatus() != SearchStatusEnum.PASSCMPLET) {
throw new IllegalStateException("Can't change to LOADING because state is " + theSearch.getStatus());
}
search.setStatus(SearchStatusEnum.LOADING);
Search newSearch = mySearchDao.save(search);
return Optional.of(newSearch);
});
} catch (Exception e) {
ourLog.warn("Failed to activate search: {}", e.toString());
ourLog.trace("Failed to activate search", e);
return Optional.empty();
}
}
@Override
public Collection<Search> findCandidatesForReuse(String theResourceType, String theQueryString, int theQueryStringHash, Date theCreatedAfter) {
int hashCode = theQueryString.hashCode();
return mySearchDao.find(theResourceType, hashCode, theCreatedAfter);
}
@Override
protected void flushLastUpdated(Long theSearchId, Date theLastUpdated) {
mySearchDao.updateSearchLastReturned(theSearchId, theLastUpdated);
}
@Transactional(Transactional.TxType.NEVER)
@Override
public void pollForStaleSearchesAndDeleteThem() {
if (!myDaoConfig.isExpireSearchResults()) {
return;
}
long cutoffMillis = myDaoConfig.getExpireSearchResultsAfterMillis();
if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null) {
cutoffMillis = Math.max(cutoffMillis, myDaoConfig.getReuseCachedSearchResultsForMillis());
}
final Date cutoff = new Date((now() - cutoffMillis) - myCutoffSlack);
if (ourNowForUnitTests != null) {
ourLog.info("Searching for searches which are before {} - now is {}", new InstantType(cutoff), new InstantType(new Date(now())));
}
ourLog.debug("Searching for searches which are before {}", cutoff);
TransactionTemplate tt = new TransactionTemplate(myTxManager);
final Slice<Long> toDelete = tt.execute(theStatus ->
mySearchDao.findWhereLastReturnedBefore(cutoff, PageRequest.of(0, 2000))
);
for (final Long nextSearchToDelete : toDelete) {
ourLog.debug("Deleting search with PID {}", nextSearchToDelete);
tt.execute(t -> {
mySearchDao.updateDeleted(nextSearchToDelete, true);
return null;
});
tt.execute(t -> {
deleteSearch(nextSearchToDelete);
return null;
});
}
int count = toDelete.getContent().size();
if (count > 0) {
if (ourLog.isDebugEnabled()) {
long total = tt.execute(t -> mySearchDao.count());
ourLog.debug("Deleted {} searches, {} remaining", count, total);
}
}
}
@VisibleForTesting
void setSearchDaoForUnitTest(ISearchDao theSearchDao) {
mySearchDao = theSearchDao;
}
@VisibleForTesting
void setSearchDaoIncludeForUnitTest(ISearchIncludeDao theSearchIncludeDao) {
mySearchIncludeDao = theSearchIncludeDao;
}
private void deleteSearch(final Long theSearchPid) {
mySearchDao.findById(theSearchPid).ifPresent(searchToDelete -> {
mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
/*
* Note, we're only deleting up to 500 results in an individual search here. This
* is to prevent really long running transactions in cases where there are
* huge searches with tons of results in them. By the time we've gotten here
* we have marked the parent Search entity as deleted, so it's not such a
* huge deal to be only partially deleting search results. They'll get deleted
* eventually
*/
int max = ourMaximumResultsToDeleteInOnePass;
Slice<Long> resultPids = mySearchResultDao.findForSearch(PageRequest.of(0, max), searchToDelete.getId());
if (resultPids.hasContent()) {
List<List<Long>> partitions = Lists.partition(resultPids.getContent(), ourMaximumResultsToDeleteInOneStatement);
for (List<Long> nextPartition : partitions) {
mySearchResultDao.deleteByIds(nextPartition);
}
}
// Only delete if we don't have results left in this search
if (resultPids.getNumberOfElements() < max) {
ourLog.debug("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), new InstantType(searchToDelete.getCreated()), new InstantType(searchToDelete.getSearchLastReturned()));
mySearchDao.deleteByPid(searchToDelete.getId());
} else {
ourLog.debug("Purged {} search results for deleted search {}/{}", resultPids.getSize(), searchToDelete.getId(), searchToDelete.getUuid());
}
});
}
@VisibleForTesting
public static void setMaximumResultsToDeleteInOnePassForUnitTest(int theMaximumResultsToDeleteInOnePass) {
ourMaximumResultsToDeleteInOnePass = theMaximumResultsToDeleteInOnePass;
}
@VisibleForTesting
public static void setMaximumResultsToDeleteForUnitTest(int theMaximumResultsToDelete) {
ourMaximumResultsToDeleteInOneStatement = theMaximumResultsToDelete;
}
/**
* This is for unit tests only, do not call otherwise
*/
@VisibleForTesting
public static void setNowForUnitTests(Long theNowForUnitTests) {
ourNowForUnitTests = theNowForUnitTests;
}
private static long now() {
if (ourNowForUnitTests != null) {
return ourNowForUnitTests;
}
return System.currentTimeMillis();
}
}

98
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchResultCacheSvcImpl.java vendored Normal file
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@ -0,0 +1,98 @@
package ca.uhn.fhir.jpa.search.cache;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchResult;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Pageable;
import javax.transaction.Transactional;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import static ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl.toPage;
public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
private static final Logger ourLog = LoggerFactory.getLogger(DatabaseSearchResultCacheSvcImpl.class);
@Autowired
private ISearchResultDao mySearchResultDao;
@Override
@Transactional(Transactional.TxType.REQUIRED)
public List<Long> fetchResultPids(Search theSearch, int theFrom, int theTo) {
final Pageable page = toPage(theFrom, theTo);
if (page == null) {
return Collections.emptyList();
}
List<Long> retVal = mySearchResultDao
.findWithSearchPid(theSearch.getId(), page)
.getContent();
ourLog.trace("fetchResultPids for range {}-{} returned {} pids", theFrom, theTo, retVal.size());
return new ArrayList<>(retVal);
}
@Override
@Transactional(Transactional.TxType.REQUIRED)
public List<Long> fetchAllResultPids(Search theSearch) {
List<Long> retVal = mySearchResultDao.findWithSearchPidOrderIndependent(theSearch.getId());
ourLog.trace("fetchAllResultPids returned {} pids", retVal.size());
return retVal;
}
@Override
@Transactional(Transactional.TxType.REQUIRED)
public void storeResults(Search theSearch, List<Long> thePreviouslyStoredResourcePids, List<Long> theNewResourcePids) {
List<SearchResult> resultsToSave = Lists.newArrayList();
ourLog.trace("Storing {} results with {} previous for search", theNewResourcePids.size(), thePreviouslyStoredResourcePids.size());
int order = thePreviouslyStoredResourcePids.size();
for (Long nextPid : theNewResourcePids) {
SearchResult nextResult = new SearchResult(theSearch);
nextResult.setResourcePid(nextPid);
nextResult.setOrder(order);
resultsToSave.add(nextResult);
ourLog.trace("Saving ORDER[{}] Resource {}", order, nextResult.getResourcePid());
order++;
}
mySearchResultDao.saveAll(resultsToSave);
}
@VisibleForTesting
void setSearchDaoResultForUnitTest(ISearchResultDao theSearchResultDao) {
mySearchResultDao = theSearchResultDao;
}
}

101
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/ISearchCacheSvc.java vendored Normal file
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@ -0,0 +1,101 @@
package ca.uhn.fhir.jpa.search.cache;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.entity.Search;
import java.util.Collection;
import java.util.Date;
import java.util.Optional;
public interface ISearchCacheSvc {
/**
* Places a new search of some sort in the cache, or updates an existing search. The search passed in is guaranteed to have
* a {@link Search#getUuid() UUID} so that is a good candidate for consistent identification.
*
* @param theSearch The search to store
* @return Returns a copy of the search as it was saved. Callers should use the returned Search object for any further processing.
*/
Search save(Search theSearch);
/**
* Fetch a search using its UUID. The search should be fully loaded when it is returned (i.e. includes are fetched, so that access to its
* fields will not cause database errors if the current tranaction scope ends.
*
* @param theUuid The search UUID
* @return The search if it exists
*/
Optional<Search> fetchByUuid(String theUuid);
/**
* TODO: this is perhaps an inappropriate responsibility for this service
*
* <p>
* This method marks a search as in progress, but should only allow exactly one call to do so across the cluster. This
* is done so that if two client threads request the next page at the exact same time (which is unlikely but not
* impossible) only one will actually proceed to load the next results and the other will just wait for them
* to arrive.
*
* @param theSearch The search to mark
* @return This method should return an empty optional if the search was not marked (meaning that another thread
* succeeded in marking it). If the search doesn't exist or some other error occurred, an exception will be thrown
* instead of {@link Optional#empty()}
*/
Optional<Search> tryToMarkSearchAsInProgress(Search theSearch);
/**
* Look for any existing searches matching the given resource type and query string.
* <p>
* This method is allowed to perofrm a "best effort" return, so it can return searches that don't match the query string exactly, or
* which have a created timestamp before <code>theCreatedAfter</code> date. The caller is responsible for removing
* any inappropriate Searches and picking the most relevant one.
* </p>
*
* @param theResourceType The resource type of the search. Results MUST match this type
* @param theQueryString The query string. Results SHOULD match this type
* @param theQueryStringHash The query string hash. Results SHOULD match this type
* @param theCreatedAfter Results SHOULD not include any searches created before this cutoff timestamp
* @return A collection of candidate searches
*/
Collection<Search> findCandidatesForReuse(String theResourceType, String theQueryString, int theQueryStringHash, Date theCreatedAfter);
/**
* Mark a search as having been "last used" at the given time. This method may (and probably should) be implemented
* to work asynchronously in order to avoid hammering the database if the search gets reused many times.
*
* @param theSearch The search
* @param theDate The "last returned" timestamp
*/
void updateSearchLastReturned(Search theSearch, Date theDate);
/**
* This is mostly public for unit tests
*/
void flushLastUpdated();
/**
* This method will be called periodically to delete stale searches. Implementations are not required to do anything
* if they have some other mechanism for expiring stale results other than manually looking for them
* and deleting them.
*/
void pollForStaleSearchesAndDeleteThem();
}

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/ISearchResultCacheSvc.java vendored Normal file
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@ -0,0 +1,51 @@
package ca.uhn.fhir.jpa.search.cache;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.entity.Search;
import java.util.List;
public interface ISearchResultCacheSvc {
/**
* @param theSearch The search - This method is not required to persist any chances to the Search object, it is only provided here for identification
* @param thePreviouslyStoredResourcePids A list of resource PIDs that have previously been saved to this search
* @param theNewResourcePids A list of new resoure PIDs to add to this search (these ones have not been previously saved)
*/
void storeResults(Search theSearch, List<Long> thePreviouslyStoredResourcePids, List<Long> theNewResourcePids);
/**
* Fetch a sunset of the search result IDs from the cache
*
* @param theSearch The search to fetch IDs for
* @param theFrom The starting index (inclusive)
* @param theTo The ending index (exclusive)
* @return A list of resource PIDs
*/
List<Long> fetchResultPids(Search theSearch, int theFrom, int theTo);
/**
* Fetch all result PIDs for a given search with no particular order required
* @param theSearch
* @return
*/
List<Long> fetchAllResultPids(Search theSearch);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -62,7 +62,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@ -88,6 +87,7 @@ import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.*;
import javax.validation.constraints.NotNull;
import java.util.*;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
View File

@ -26,7 +26,9 @@ import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;

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

@ -6,7 +6,9 @@ import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import javax.annotation.Nullable;
import java.util.List;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
View File

@ -34,9 +34,9 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import javax.validation.constraints.NotNull;
import java.io.*;
import java.util.*;
import java.util.Map.Entry;

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -5,23 +5,25 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.ExpungeOptions;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.test.utilities.LoggingRule;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.utilities.LoggingRule;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.TestUtil;
@ -91,6 +93,10 @@ public abstract class BaseJpaTest {
protected IInterceptorService myInterceptorRegistry;
@Autowired
protected CircularQueueCaptureQueriesListener myCaptureQueriesListener;
@Autowired
protected ISearchResultCacheSvc mySearchResultCacheSvc;
@Autowired
protected ISearchCacheSvc mySearchCacheSvc;
@After
public void afterPerformCleanup() {

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -206,8 +206,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired(required = false)
protected IFulltextSearchSvc mySearchDao;
@Autowired
protected ISearchDao mySearchEntityDao;
@Autowired
@Qualifier("mySearchParameterDaoDstu3")
protected IFhirResourceDao<SearchParameter> mySearchParameterDao;
@Autowired

401
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchPageExpiryTest.java
View File

@ -1,401 +0,0 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4SearchPageExpiryTest;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.model.InstantType;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.lang.Nullable;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.util.Date;
import java.util.concurrent.atomic.AtomicLong;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.*;
public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoDstu3SearchPageExpiryTest.class);
@After()
public void after() {
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
StaleSearchDeletingSvcImpl.setNowForUnitTests(null);
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
myDaoConfig.setExpireSearchResults(new DaoConfig().isExpireSearchResults());
}
@Before
public void before() {
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
myDaoConfig.setExpireSearchResults(new DaoConfig().isExpireSearchResults());
myDaoConfig.setCountSearchResultsUpTo(null);
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
}
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
public void testExpirePagesAfterReuse() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
long start = System.currentTimeMillis();
final String searchUuid1;
{
SearchParameterMap params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
searchUuid1 = bundleProvider.getUuid();
Validate.notBlank(searchUuid1);
}
waitForSearchToSave(searchUuid1);
final String searchUuid2;
{
SearchParameterMap params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
searchUuid2 = bundleProvider.getUuid();
Validate.notBlank(searchUuid2);
}
assertEquals(searchUuid1, searchUuid2);
TestUtil.sleepAtLeast(501);
// We're now past 500ms so we shouldn't reuse the search
final String searchUuid3;
{
SearchParameterMap params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
searchUuid3 = bundleProvider.getUuid();
Validate.notBlank(searchUuid3);
}
assertNotEquals(searchUuid1, searchUuid3);
// Search just got used so it shouldn't be deleted
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 500);
final AtomicLong search3timestamp = new AtomicLong();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search3 = mySearchEntityDao.findByUuid(searchUuid3);
assertNotNull(search3);
Search search2 = mySearchEntityDao.findByUuid(searchUuid2);
assertNotNull(search2);
search3timestamp.set(search2.getSearchLastReturned().getTime());
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 800);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
}
});
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid1));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull("Search 1 still exists", mySearchEntityDao.findByUuid(searchUuid1));
assertNotNull("Search 3 still exists", mySearchEntityDao.findByUuid(searchUuid3));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 2100);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull("Search 1 still exists", mySearchEntityDao.findByUuid(searchUuid1));
assertNull("Search 3 still exists", mySearchEntityDao.findByUuid(searchUuid3));
}
});
}
@Test
public void testExpirePagesAfterSingleUse() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
final StopWatch sw = new StopWatch();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
waitForSearchToSave(bundleProvider.getUuid());
final AtomicLong start = new AtomicLong();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = mySearchEntityDao.findByUuid(bundleProvider.getUuid());
assertNotNull("Failed after " + sw.toString(), search);
start.set(search.getCreated().getTime());
ourLog.info("Search was created: {}", new InstantType(new Date(start.get())));
}
});
myDaoConfig.setExpireSearchResultsAfterMillis(500);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start.get() + 499);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start.get() + 600);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
}
@Test
public void testExpirePagesAfterSingleUse2() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
long start = System.currentTimeMillis();
final String searchUuid1;
{
SearchParameterMap params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
searchUuid1 = bundleProvider.getUuid();
Validate.notBlank(searchUuid1);
}
String searchUuid2;
{
SearchParameterMap params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
searchUuid2 = bundleProvider.getUuid();
Validate.notBlank(searchUuid2);
}
assertEquals(searchUuid1, searchUuid2);
TestUtil.sleepAtLeast(501);
// We're now past 500ms so we shouldn't reuse the search
final String searchUuid3;
{
SearchParameterMap params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
searchUuid3 = bundleProvider.getUuid();
Validate.notBlank(searchUuid3);
}
assertNotEquals(searchUuid1, searchUuid3);
// Search just got used so it shouldn't be deleted
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
final AtomicLong search3timestamp = new AtomicLong();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search3 = mySearchEntityDao.findByUuid(searchUuid3);
assertNotNull(search3);
search3timestamp.set(search3.getCreated().getTime());
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 800);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
}
});
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(searchUuid1));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull("Search 1 still exists", mySearchEntityDao.findByUuid(searchUuid1));
assertNull("Search 3 still exists", mySearchEntityDao.findByUuid(searchUuid3));
}
});
}
@Test
public void testSearchPagesExpiryDisabled() throws Exception {
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
params.setCount(1);
final IBundleProvider bundleProvider = myPatientDao.search(params);
Search search = null;
for (int i = 0; i < 100 && search == null; i++) {
search = newTxTemplate().execute(new TransactionCallback<Search>() {
@Nullable
@Override
public Search doInTransaction(TransactionStatus status) {
return mySearchEntityDao.findByUuid(bundleProvider.getUuid());
}
});
if (search == null) {
TestUtil.sleepAtLeast(100);
}
}
assertNotNull("Search " + bundleProvider.getUuid() + " not found on disk after 10 seconds", search);
myDaoConfig.setExpireSearchResults(false);
StaleSearchDeletingSvcImpl.setNowForUnitTests(System.currentTimeMillis() + DateUtils.MILLIS_PER_DAY);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = mySearchEntityDao.findByUuid(bundleProvider.getUuid());
assertNotNull(search);
}
});
myDaoConfig.setExpireSearchResults(true);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = mySearchEntityDao.findByUuid(bundleProvider.getUuid());
assertNull(search);
}
});
}
private void waitForSearchToSave(final String theUuid) {
final ISearchDao searchEntityDao = mySearchEntityDao;
TransactionTemplate txTemplate = newTxTemplate();
FhirResourceDaoR4SearchPageExpiryTest.waitForSearchToSave(theUuid, searchEntityDao, txTemplate);
}
}

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.config.TestR4Config;
import ca.uhn.fhir.jpa.dao.*;
@ -11,7 +12,6 @@ import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
@ -21,7 +21,6 @@ import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.BaseSearchParamRegistry;
import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionRegistry;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
@ -57,7 +56,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.PlatformTransactionManager;
@ -251,12 +249,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Autowired(required = false)
protected IFulltextSearchSvc mySearchDao;
@Autowired
protected ISearchDao mySearchEntityDao;
@Autowired
protected ISearchResultDao mySearchResultDao;
@Autowired
protected ISearchIncludeDao mySearchIncludeDao;
@Autowired
protected IResourceReindexJobDao myResourceReindexJobDao;
@Autowired
@Qualifier("mySearchParameterDaoR4")

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -55,6 +56,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
@Autowired
MatchUrlService myMatchUrlService;
@Autowired
private ISearchDao mySearchEntityDao;
@After
public void afterResetSearchSize() {

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java
View File

@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@ -30,6 +30,7 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@ -49,6 +50,8 @@ import static org.mockito.Mockito.mock;
@SuppressWarnings({"unchecked", "Duplicates"})
public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchNoHashesTest.class);
@Autowired
private ISearchDao mySearchEntityDao;
@After
public void afterResetSearchSize() {

34
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
View File

@ -1,6 +1,8 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
@ -14,6 +16,7 @@ import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -24,6 +27,7 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.aop.framework.AopProxyUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.concurrent.ThreadPoolExecutorFactoryBean;
import org.springframework.test.context.TestPropertySource;
@ -48,6 +52,10 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchOptimizedTest.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcImpl;
@Autowired
private ISearchDao mySearchEntityDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Before
public void before() {
@ -288,7 +296,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(200, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertNull(search.getTotalCount());
@ -307,7 +315,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* Search gets incremented twice as a part of loading the next batch
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(SearchStatusEnum.FINISHED, search.getStatus());
assertEquals(200, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
@ -343,7 +351,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(20, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertNull(search.getTotalCount());
@ -367,7 +375,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* Search should be untouched
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(1, search.getVersion().intValue());
});
@ -383,7 +391,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* Search gets incremented twice as a part of loading the next batch
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
assertEquals(50, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
@ -407,7 +415,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* Search should be untouched
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(3, search.getVersion().intValue());
});
@ -423,7 +431,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* Search gets incremented twice as a part of loading the next batch
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(190, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertEquals(190, search.getTotalCount().intValue());
@ -470,7 +478,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(50, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertEquals(null, search.getTotalCount());
@ -505,7 +513,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(20, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertNull(search.getTotalCount());
@ -529,7 +537,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* Search should be untouched
*/
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(200, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertEquals(200, search.getTotalCount().intValue());
@ -562,9 +570,9 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
* 20 should be prefetched since that's the initial page size
*/
waitForSize(20, () -> runInTransaction(() -> mySearchEntityDao.findByUuid(uuid).getNumFound()));
waitForSize(20, () -> runInTransaction(() -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException("")).getNumFound()));
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(20, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());
assertNull(search.getTotalCount());
@ -625,7 +633,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
assertEquals(1, ids.size());
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuid(uuid);
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(SearchStatusEnum.FINISHED, search.getStatus());
assertEquals(1, search.getNumFound());
assertEquals(search.getNumFound(), mySearchResultDao.count());

80
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java
View File

@ -1,15 +1,16 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IIdType;
@ -20,6 +21,7 @@ import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
@ -30,6 +32,7 @@ import javax.annotation.Nullable;
import java.util.Date;
import java.util.concurrent.atomic.AtomicLong;
import static ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl.DEFAULT_CUTOFF_SLACK;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.*;
@ -37,16 +40,19 @@ import static org.junit.Assert.*;
public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchPageExpiryTest.class);
@Autowired
private ISearchDao mySearchEntityDao;
@After()
public void after() {
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
StaleSearchDeletingSvcImpl.setNowForUnitTests(null);
DatabaseSearchCacheSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(mySearchCacheSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(DEFAULT_CUTOFF_SLACK);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(null);
}
@Before
public void before() {
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
DatabaseSearchCacheSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(mySearchCacheSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
}
@ -77,7 +83,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
long start = System.currentTimeMillis();
StaleSearchDeletingSvcImpl.setNowForUnitTests(start);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(start);
final String searchUuid1;
{
@ -117,53 +123,53 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
// Search just got used so it shouldn't be deleted
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 500);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(start + 500);
final AtomicLong search3timestamp = new AtomicLong();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search3 = mySearchEntityDao.findByUuid(searchUuid3);
Search search3 = mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3).orElseThrow(()->new InternalErrorException("Search doesn't exist"));
assertNotNull(search3);
Search search2 = mySearchEntityDao.findByUuid(searchUuid2);
Search search2 = mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid2).orElseThrow(()->new InternalErrorException("Search doesn't exist"));
assertNotNull(search2);
search3timestamp.set(search2.getSearchLastReturned().getTime());
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 800);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 800);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
assertNotNull(mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3));
}
});
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid1));
assertNotNull(mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid1));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull("Search 1 still exists", mySearchEntityDao.findByUuid(searchUuid1));
assertNotNull("Search 3 still exists", mySearchEntityDao.findByUuid(searchUuid3));
assertFalse("Search 1 still exists", mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid1).isPresent());
assertTrue("Search 3 still exists", mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3).isPresent());
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 2100);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 2100);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull("Search 1 still exists", mySearchEntityDao.findByUuid(searchUuid1));
assertNull("Search 3 still exists", mySearchEntityDao.findByUuid(searchUuid3));
assertFalse("Search 1 still exists", mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid1).isPresent());
assertFalse("Search 3 still exists", mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3).isPresent());
}
});
@ -202,7 +208,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = mySearchEntityDao.findByUuid(bundleProvider.getUuid());
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(bundleProvider.getUuid()).orElseThrow(()->new InternalErrorException("Search doesn't exist"));
assertNotNull("Failed after " + sw.toString(), search);
start.set(search.getCreated().getTime());
ourLog.info("Search was created: {}", new InstantType(new Date(start.get())));
@ -211,21 +217,21 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
myDaoConfig.setExpireSearchResultsAfterMillis(500);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start.get() + 499);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(start.get() + 499);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
assertNotNull(mySearchEntityDao.findByUuidAndFetchIncludes(bundleProvider.getUuid()));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start.get() + 600);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(start.get() + 600);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
assertFalse(mySearchEntityDao.findByUuidAndFetchIncludes(bundleProvider.getUuid()).isPresent());
}
});
}
@ -296,36 +302,36 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search3 = mySearchEntityDao.findByUuid(searchUuid3);
Search search3 = mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3).orElseThrow(()->new InternalErrorException("Search doesn't exist"));
assertNotNull(search3);
search3timestamp.set(search3.getCreated().getTime());
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 800);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 800);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
assertNotNull(mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3));
}
});
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(searchUuid1));
assertFalse(mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid1).isPresent());
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull("Search 1 still exists", mySearchEntityDao.findByUuid(searchUuid1));
assertNull("Search 3 still exists", mySearchEntityDao.findByUuid(searchUuid3));
assertFalse("Search 1 still exists", mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid1).isPresent());
assertFalse("Search 3 still exists", mySearchEntityDao.findByUuidAndFetchIncludes(searchUuid3).isPresent());
}
});
@ -356,7 +362,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
@Nullable
@Override
public Search doInTransaction(TransactionStatus status) {
return mySearchEntityDao.findByUuid(bundleProvider.getUuid());
return mySearchEntityDao.findByUuidAndFetchIncludes(bundleProvider.getUuid()).orElse(null);
}
});
if (search == null) {
@ -367,13 +373,13 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
myDaoConfig.setExpireSearchResults(false);
StaleSearchDeletingSvcImpl.setNowForUnitTests(System.currentTimeMillis() + DateUtils.MILLIS_PER_DAY);
DatabaseSearchCacheSvcImpl.setNowForUnitTests(System.currentTimeMillis() + DateUtils.MILLIS_PER_DAY);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = mySearchEntityDao.findByUuid(bundleProvider.getUuid());
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(bundleProvider.getUuid()).orElseThrow(()->new InternalErrorException("Search doesn't exist"));
assertNotNull(search);
}
});
@ -386,7 +392,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = mySearchEntityDao.findByUuid(bundleProvider.getUuid());
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(bundleProvider.getUuid()).orElse(null);
assertNull(search);
}
});
@ -405,7 +411,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search search = null;
for (int i = 0; i < 20 && search == null; i++) {
search = theSearchEntityDao.findByUuid(theUuid);
search = theSearchEntityDao.findByUuidAndFetchIncludes(theUuid).orElse(null);
if (search == null || search.getStatus() == SearchStatusEnum.LOADING) {
TestUtil.sleepAtLeast(100);
}

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

@ -3860,7 +3860,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
search.setStatus(SearchStatusEnum.FAILED);
search.setFailureCode(500);
search.setFailureMessage("FOO");
mySearchEntityDao.save(search);
mySearchCacheSvc.save(search);
});
IBundleProvider results = myEncounterDao.search(map);

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
View File

@ -249,12 +249,6 @@ public abstract class BaseJpaR5Test extends BaseJpaTest {
@Autowired(required = false)
protected IFulltextSearchSvc mySearchDao;
@Autowired
protected ISearchDao mySearchEntityDao;
@Autowired
protected ISearchResultDao mySearchResultDao;
@Autowired
protected ISearchIncludeDao mySearchIncludeDao;
@Autowired
protected IResourceReindexJobDao myResourceReindexJobDao;
@Autowired
@Qualifier("mySearchParameterDaoR5")

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/BaseResourceProviderDstu2Test.java
View File

@ -13,6 +13,7 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
@ -36,8 +37,6 @@ import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import ca.uhn.fhir.test.utilities.JettyUtil;
public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
protected static IGenericClient ourClient;
@ -61,12 +60,12 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
}
@SuppressWarnings({ "unchecked", "rawtypes" })
@SuppressWarnings({"unchecked", "rawtypes"})
@Before
public void before() throws Exception {
myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
myFhirCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
if (ourServer == null) {
ourRestServer = new RestfulServer(myFhirCtx);
ourRestServer.registerProviders(myResourceProviders.createProviders());
@ -82,7 +81,7 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
ourConnectionPoolSize = myAppCtx.getBean("maxDatabaseThreadsForTest", Integer.class);
ourRestServer.setPagingProvider(ourPagingProvider);
Server server = new Server(ourPort);
Server server = new Server(0);
ServletContextHandler proxyHandler = new ServletContextHandler();
proxyHandler.setContextPath("/");
@ -103,16 +102,14 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
ServletHolder subsServletHolder = new ServletHolder();
subsServletHolder.setServlet(dispatcherServlet);
subsServletHolder.setInitParameter(
ContextLoader.CONFIG_LOCATION_PARAM,
WebsocketDispatcherConfig.class.getName());
subsServletHolder.setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, WebsocketDispatcherConfig.class.getName());
proxyHandler.addServlet(subsServletHolder, "/*");
server.setHandler(proxyHandler);
JettyUtil.startServer(server);
ourPort = JettyUtil.getPortForStartedServer(server);
ourServerBase = "http://localhost:" + ourPort + "/fhir/context";
ourPort = JettyUtil.getPortForStartedServer(server);
ourServerBase = "http://localhost:" + ourPort + "/fhir/context";
ourClient = myFhirCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor());

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/GraphQLR4ProviderTest.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/JpaGraphQLR4ProviderTest.java
View File

@ -44,9 +44,11 @@ import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
public class GraphQLR4ProviderTest {
public class JpaGraphQLR4ProviderTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GraphQLR4ProviderTest.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaGraphQLR4ProviderTest.class);
public static final String DATA_PREFIX = "{\"data\": ";
public static final String DATA_SUFFIX = "}";
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forR4();
private static int ourPort;
@ -67,14 +69,14 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"name\":[{\n" +
" \"family\":\"FAMILY\",\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
" },{\n" +
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
@ -93,12 +95,12 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"name\":[{\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
" \"family\":\"FAMILY\"\n" +
" }]\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
@ -117,7 +119,7 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"Patient\":{\n" +
" \"name\":[{\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
@ -126,7 +128,7 @@ public class GraphQLR4ProviderTest {
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
" }\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
@ -145,7 +147,7 @@ public class GraphQLR4ProviderTest {
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"PatientList\":[{\n" +
" \"name\":[{\n" +
" \"family\":\"pet\",\n" +
@ -158,7 +160,7 @@ public class GraphQLR4ProviderTest {
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(responseContent));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java
View File

@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
@ -18,6 +17,7 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
@ -48,8 +48,6 @@ import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import ca.uhn.fhir.test.utilities.JettyUtil;
public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
@ -62,7 +60,6 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
protected static GenericWebApplicationContext ourWebApplicationContext;
protected static SearchParamRegistryDstu3 ourSearchParamRegistry;
protected static DatabaseBackedPagingProvider ourPagingProvider;
protected static ISearchDao mySearchEntityDao;
protected static ISearchCoordinatorSvc ourSearchCoordinatorSvc;
private static Server ourServer;
protected static SubscriptionTriggeringProvider ourSubscriptionTriggeringProvider;
@ -156,7 +153,6 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
WebApplicationContext wac = WebApplicationContextUtils.getWebApplicationContext(subsServletHolder.getServlet().getServletConfig().getServletContext());
myValidationSupport = wac.getBean(JpaValidationSupportChainDstu3.class);
ourSearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
mySearchEntityDao = wac.getBean(ISearchDao.class);
ourSearchParamRegistry = wac.getBean(SearchParamRegistryDstu3.class);
ourSubscriptionTriggeringProvider = wac.getBean(SubscriptionTriggeringProvider.class);

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/GraphQLProviderDstu3Test.java
View File

@ -5,8 +5,8 @@ import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -14,6 +14,8 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_PREFIX;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_SUFFIX;
import static org.junit.Assert.assertEquals;
public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
@ -30,14 +32,14 @@ public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX +"{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
" },{\n" +
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}
@ -52,7 +54,7 @@ public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX +"{\n" +
" \"PatientList\":[{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
@ -65,7 +67,7 @@ public class GraphQLProviderDstu3Test extends BaseResourceProviderDstu3Test {
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}

36
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.provider.r4.ResourceProviderR4Test;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
@ -18,10 +19,7 @@ import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
@ -51,7 +49,11 @@ import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
@ -74,6 +76,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3Test.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
@Autowired
private ISearchDao mySearchEntityDao;
@Override
@After
@ -2969,12 +2973,13 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
.count(5)
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid1 = toSearchUuidFromLinkNext(result1);
Search search1 = newTxTemplate().execute(new TransactionCallback<Search>() {
@Override
public Search doInTransaction(TransactionStatus theStatus) {
return mySearchEntityDao.findByUuid(uuid1);
return mySearchEntityDao.findByUuidAndFetchIncludes(uuid1).orElseThrow(() -> new InternalErrorException(""));
}
});
Date lastReturned1 = search1.getSearchLastReturned();
@ -2986,12 +2991,13 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
.count(5)
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid2 = toSearchUuidFromLinkNext(result2);
Search search2 = newTxTemplate().execute(new TransactionCallback<Search>() {
@Override
public Search doInTransaction(TransactionStatus theStatus) {
return mySearchEntityDao.findByUuid(uuid2);
return mySearchEntityDao.findByUuidAndFetchIncludes(uuid2).orElseThrow(() -> new InternalErrorException(""));
}
});
Date lastReturned2 = search2.getSearchLastReturned();
@ -3031,14 +3037,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
.forResource("Organization")
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid1 = toSearchUuidFromLinkNext(result1);
Search search1 = newTxTemplate().execute(new TransactionCallback<Search>() {
@Override
public Search doInTransaction(TransactionStatus theStatus) {
return mySearchEntityDao.findByUuid(uuid1);
}
});
Search search1 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid1).orElseThrow(() -> new InternalErrorException("")));
Date lastReturned1 = search1.getSearchLastReturned();
Bundle result2 = ourClient
@ -3046,14 +3048,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
.forResource("Organization")
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid2 = toSearchUuidFromLinkNext(result2);
Search search2 = newTxTemplate().execute(new TransactionCallback<Search>() {
@Override
public Search doInTransaction(TransactionStatus theStatus) {
return mySearchEntityDao.findByUuid(uuid2);
}
});
Search search2 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid2).orElseThrow(() -> new InternalErrorException("")));
Date lastReturned2 = search2.getSearchLastReturned();
assertTrue(lastReturned2.getTime() > lastReturned1.getTime());

97
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/StaleSearchDeletingSvcDstu3Test.java
View File

@ -1,97 +0,0 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.hamcrest.Matchers.blankOrNullString;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.dstu3.model.Patient;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.test.util.AopTestUtils;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.rest.gclient.IClientExecutable;
import ca.uhn.fhir.rest.gclient.IQuery;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.util.TestUtil;
public class StaleSearchDeletingSvcDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StaleSearchDeletingSvcDstu3Test.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@After()
public void after() throws Exception {
super.after();
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
}
@Before
public void before() throws Exception {
super.before();
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
}
@Test
public void testEverythingInstanceWithContentFilter() throws Exception {
for (int i = 0; i < 20; i++) {
Patient pt1 = new Patient();
pt1.addName().setFamily("Everything").addGiven("Arthur");
myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless();
}
//@formatter:off
IClientExecutable<IQuery<Bundle>, Bundle> search = ourClient
.search()
.forResource(Patient.class)
.where(Patient.NAME.matches().value("Everything"))
.returnBundle(Bundle.class);
//@formatter:on
Bundle resp1 = search.execute();
for (int i = 0; i < 20; i++) {
search.execute();
}
BundleLinkComponent nextLink = resp1.getLink("next");
assertNotNull(nextLink);
String nextLinkUrl = nextLink.getUrl();
assertThat(nextLinkUrl, not(blankOrNullString()));
Bundle resp2 = ourClient.search().byUrl(nextLinkUrl).returnBundle(Bundle.class).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp2));
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
ourClient.search().byUrl(nextLinkUrl).returnBundle(Bundle.class).execute();
Thread.sleep(20);
myDaoConfig.setExpireSearchResultsAfterMillis(10);
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
try {
ourClient.search().byUrl(nextLinkUrl).returnBundle(Bundle.class).execute();
fail();
} catch (ResourceGoneException e) {
assertThat(e.getMessage(), containsString("does not exist and may have expired"));
}
}
}

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
View File

@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig;
import ca.uhn.fhir.jpa.dao.DaoRegistry;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ExpungeR4Test.java
View File

@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.ExpungeOptions;
@ -21,6 +23,7 @@ import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
@ -38,6 +41,10 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
private IIdType myOneVersionObservationId;
private IIdType myTwoVersionObservationId;
private IIdType myDeletedObservationId;
@Autowired
private ISearchDao mySearchEntityDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@After
public void afterDisableExpunge() {

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLProviderR4Test.java
View File

@ -14,6 +14,8 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_PREFIX;
import static ca.uhn.fhir.jpa.provider.JpaGraphQLR4ProviderTest.DATA_SUFFIX;
import static org.junit.Assert.assertEquals;
public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
@ -30,14 +32,14 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
" \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
" },{\n" +
" \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}
@ -52,7 +54,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(TestUtil.stripReturns("{\n" +
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"PatientList\":[{\n" +
" \"name\":[{\n" +
" \"family\":\"FAM\",\n" +
@ -65,7 +67,7 @@ public class GraphQLProviderR4Test extends BaseResourceProviderR4Test {
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}"), TestUtil.stripReturns(resp));
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
}
}

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CacheTest.java
View File

@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.CacheControlDirective;
@ -13,9 +13,8 @@ import org.hl7.fhir.r4.model.Patient;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
import org.springframework.test.util.AopTestUtils;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Date;
import static org.hamcrest.Matchers.*;
@ -24,9 +23,9 @@ import static org.junit.Assert.*;
public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CacheTest.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
private CapturingInterceptor myCapturingInterceptor;
@Autowired
private ISearchDao mySearchEntityDao;
@Override
@After
@ -42,14 +41,13 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
public void before() throws Exception {
super.before();
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
mySearchCoordinatorSvcRaw = AopTestUtils.getTargetObject(mySearchCoordinatorSvc);
myCapturingInterceptor = new CapturingInterceptor();
ourClient.registerInterceptor(myCapturingInterceptor);
}
@Test
public void testCacheNoStore() throws IOException {
public void testCacheNoStore() {
Patient pt1 = new Patient();
pt1.addName().setFamily("FAM");
@ -84,7 +82,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
}
@Test
public void testCacheNoStoreMaxResults() throws IOException {
public void testCacheNoStoreMaxResults() {
for (int i = 0; i < 10; i++) {
Patient pt1 = new Patient();
@ -106,7 +104,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
}
@Test
public void testCacheNoStoreMaxResultsWithIllegalValue() throws IOException {
public void testCacheNoStoreMaxResultsWithIllegalValue() {
myDaoConfig.setCacheControlNoStoreMaxResultsUpperLimit(123);
try {
ourClient
@ -123,7 +121,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
}
@Test
public void testCacheSuppressed() throws IOException {
public void testCacheSuppressed() {
Patient pt1 = new Patient();
pt1.addName().setFamily("FAM");
@ -152,7 +150,7 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
}
@Test
public void testCacheUsedNormally() throws IOException {
public void testCacheUsedNormally() {
Patient pt1 = new Patient();
pt1.addName().setFamily("FAM");

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -2,10 +2,11 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.config.TestR4Config;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.primitive.InstantDt;
@ -21,10 +22,7 @@ import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
@ -54,6 +52,7 @@ import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@ -82,6 +81,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public static final int LARGE_NUMBER = 77;
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
@Autowired
private ISearchDao mySearchEntityDao;
@Override
@After
@ -3937,9 +3938,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.count(5)
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid1 = toSearchUuidFromLinkNext(result1);
Search search1 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuid(uuid1));
Search search1 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid1).orElseThrow(()->new InternalErrorException("")));
Date lastReturned1 = search1.getSearchLastReturned();
Bundle result2 = ourClient
@ -3949,9 +3951,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.count(5)
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid2 = toSearchUuidFromLinkNext(result2);
Search search2 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuid(uuid2));
Search search2 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid2).orElseThrow(()->new InternalErrorException("")));
Date lastReturned2 = search2.getSearchLastReturned();
assertTrue(lastReturned2.getTime() > lastReturned1.getTime());
@ -3965,6 +3968,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.count(5)
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
String uuid3 = toSearchUuidFromLinkNext(result3);
@ -3989,9 +3993,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.forResource("Organization")
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid1 = toSearchUuidFromLinkNext(result1);
Search search1 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuid(uuid1));
Search search1 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid1).orElseThrow(()->new InternalErrorException("")));
Date lastReturned1 = search1.getSearchLastReturned();
sleepOneClick();
@ -4001,9 +4006,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.forResource("Organization")
.returnBundle(Bundle.class)
.execute();
mySearchCacheSvc.flushLastUpdated();
final String uuid2 = toSearchUuidFromLinkNext(result2);
Search search2 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuid(uuid2));
Search search2 = newTxTemplate().execute(theStatus -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid2).orElseThrow(()->new InternalErrorException("")));
Date lastReturned2 = search2.getSearchLastReturned();
assertTrue(lastReturned2.getTime() > lastReturned1.getTime());

36
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/StaleSearchDeletingSvcR4Test.java
View File

@ -1,9 +1,15 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.entity.SearchResult;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.rest.gclient.IClientExecutable;
import ca.uhn.fhir.rest.gclient.IQuery;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
@ -16,6 +22,7 @@ import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
import java.util.Date;
@ -27,22 +34,28 @@ import static org.junit.Assert.*;
public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StaleSearchDeletingSvcR4Test.class);
@Autowired
private ISearchDao mySearchEntityDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Autowired
private ISearchIncludeDao mySearchIncludeDao;
@Override
@After()
public void after() throws Exception {
super.after();
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
StaleSearchDeletingSvcImpl.setMaximumResultsToDeleteForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT);
StaleSearchDeletingSvcImpl.setMaximumResultsToDeleteInOnePassForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS);
DatabaseSearchCacheSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(mySearchCacheSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(DatabaseSearchCacheSvcImpl.DEFAULT_CUTOFF_SLACK);
DatabaseSearchCacheSvcImpl.setMaximumResultsToDeleteForUnitTest(DatabaseSearchCacheSvcImpl.DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT);
DatabaseSearchCacheSvcImpl.setMaximumResultsToDeleteInOnePassForUnitTest(DatabaseSearchCacheSvcImpl.DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS);
}
@Override
@Before
public void before() throws Exception {
super.before();
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
DatabaseSearchCacheSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(mySearchCacheSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
}
@ -96,8 +109,8 @@ public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
@Test
public void testDeleteVeryLargeSearch() {
StaleSearchDeletingSvcImpl.setMaximumResultsToDeleteForUnitTest(10);
StaleSearchDeletingSvcImpl.setMaximumResultsToDeleteInOnePassForUnitTest(10);
DatabaseSearchCacheSvcImpl.setMaximumResultsToDeleteForUnitTest(10);
DatabaseSearchCacheSvcImpl.setMaximumResultsToDeleteInOnePassForUnitTest(10);
runInTransaction(() -> {
Search search = new Search();
@ -139,7 +152,7 @@ public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
@Test
public void testDeleteVerySmallSearch() {
StaleSearchDeletingSvcImpl.setMaximumResultsToDeleteForUnitTest(10);
DatabaseSearchCacheSvcImpl.setMaximumResultsToDeleteForUnitTest(10);
runInTransaction(() -> {
Search search = new Search();
@ -149,8 +162,7 @@ public class StaleSearchDeletingSvcR4Test extends BaseResourceProviderR4Test {
search.setSearchType(SearchTypeEnum.SEARCH);
search.setResourceType("Patient");
search.setSearchLastReturned(DateUtils.addDays(new Date(), -10000));
search = mySearchEntityDao.save(search);
mySearchEntityDao.save(search);
});
// It should take one pass to delete the search fully

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/BaseResourceProviderR5Test.java
View File

@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.provider.r5;
import ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig;
import ca.uhn.fhir.jpa.dao.DaoRegistry;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.r5.BaseJpaR5Test;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
@ -64,7 +63,6 @@ public abstract class BaseResourceProviderR5Test extends BaseJpaR5Test {
protected static String ourServerBase;
protected static SearchParamRegistryR5 ourSearchParamRegistry;
private static DatabaseBackedPagingProvider ourPagingProvider;
protected static ISearchDao mySearchEntityDao;
protected static ISearchCoordinatorSvc mySearchCoordinatorSvc;
private static GenericWebApplicationContext ourWebApplicationContext;
private static SubscriptionMatcherInterceptor ourSubscriptionMatcherInterceptor;
@ -166,7 +164,6 @@ public abstract class BaseResourceProviderR5Test extends BaseJpaR5Test {
WebApplicationContext wac = WebApplicationContextUtils.getWebApplicationContext(subsServletHolder.getServlet().getServletConfig().getServletContext());
myValidationSupport = wac.getBean(JpaValidationSupportChainR5.class);
mySearchCoordinatorSvc = wac.getBean(ISearchCoordinatorSvc.class);
mySearchEntityDao = wac.getBean(ISearchDao.class);
ourSearchParamRegistry = wac.getBean(SearchParamRegistryR5.class);
ourSubscriptionMatcherInterceptor = wac.getBean(SubscriptionMatcherInterceptor.class);
ourSubscriptionMatcherInterceptor.start();

122
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
View File

@ -3,13 +3,11 @@ package ca.uhn.fhir.jpa.search;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchResult;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.BaseIterator;
import ca.uhn.fhir.model.dstu2.resource.Patient;
@ -19,7 +17,6 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.After;
import org.junit.AfterClass;
@ -34,7 +31,6 @@ import org.mockito.junit.MockitoJUnitRunner;
import org.mockito.stubbing.Answer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.data.domain.PageImpl;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionStatus;
@ -53,20 +49,18 @@ public class SearchCoordinatorSvcImplTest {
private static final Logger ourLog = LoggerFactory.getLogger(SearchCoordinatorSvcImplTest.class);
private static FhirContext ourCtx = FhirContext.forDstu3();
@Captor
ArgumentCaptor<Iterable<SearchResult>> mySearchResultIterCaptor;
ArgumentCaptor<List<Long>> mySearchResultIterCaptor;
@Mock
private IFhirResourceDao<?> myCallingDao;
@Mock
private EntityManager myEntityManager;
private int myExpectedNumberOfSearchBuildersCreated = 2;
@Mock
private ISearchBuilder mySearchBuider;
private ISearchBuilder mySearchBuilder;
@Mock
private ISearchDao mySearchDao;
private ISearchCacheSvc mySearchCacheSvc;
@Mock
private ISearchIncludeDao mySearchIncludeDao;
@Mock
private ISearchResultDao mySearchResultDao;
private ISearchResultCacheSvc mySearchResultCacheSvc;
private SearchCoordinatorSvcImpl mySvc;
@Mock
private PlatformTransactionManager myTxManager;
@ -90,16 +84,14 @@ public class SearchCoordinatorSvcImplTest {
mySvc.setEntityManagerForUnitTest(myEntityManager);
mySvc.setTransactionManagerForUnitTest(myTxManager);
mySvc.setContextForUnitTest(ourCtx);
mySvc.setSearchDaoForUnitTest(mySearchDao);
mySvc.setSearchDaoIncludeForUnitTest(mySearchIncludeDao);
mySvc.setSearchDaoResultForUnitTest(mySearchResultDao);
mySvc.setSearchCacheServicesForUnitTest(mySearchCacheSvc, mySearchResultCacheSvc);
mySvc.setDaoRegistryForUnitTest(myDaoRegistry);
mySvc.setInterceptorBroadcasterForUnitTest(myInterceptorBroadcaster);
myDaoConfig = new DaoConfig();
mySvc.setDaoConfigForUnitTest(myDaoConfig);
when(myCallingDao.newSearchBuilder()).thenReturn(mySearchBuider);
when(myCallingDao.newSearchBuilder()).thenReturn(mySearchBuilder);
when(myTxManager.getTransaction(any())).thenReturn(mock(TransactionStatus.class));
@ -107,7 +99,7 @@ public class SearchCoordinatorSvcImplTest {
PersistedJpaBundleProvider provider = (PersistedJpaBundleProvider) theInvocation.getArguments()[0];
provider.setSearchCoordinatorSvc(mySvc);
provider.setPlatformTransactionManager(myTxManager);
provider.setSearchDao(mySearchDao);
provider.setSearchCacheSvc(mySearchCacheSvc);
provider.setEntityManager(myEntityManager);
provider.setContext(ourCtx);
provider.setInterceptorBroadcaster(myInterceptorBroadcaster);
@ -143,7 +135,7 @@ public class SearchCoordinatorSvcImplTest {
List<Long> pids = createPidSequence(10, 800);
IResultIterator iter = new FailAfterNIterator(new SlowIterator(pids.iterator(), 2), 300);
when(mySearchBuider.createQuery(Mockito.same(params), any(), any())).thenReturn(iter);
when(mySearchBuilder.createQuery(Mockito.same(params), any(), any())).thenReturn(iter);
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNotNull(result.getUuid());
@ -159,23 +151,42 @@ public class SearchCoordinatorSvcImplTest {
@Test
public void testAsyncSearchLargeResultSetBigCountSameCoordinator() {
List<Long> allResults = new ArrayList<>();
doAnswer(t->{
List<Long> oldResults = t.getArgument(1, List.class);
List<Long> newResults = t.getArgument(2, List.class);
ourLog.info("Saving {} new results - have {} old results", newResults.size(), oldResults.size());
assertEquals(allResults.size(), oldResults.size());
allResults.addAll(newResults);
return null;
}).when(mySearchResultCacheSvc).storeResults(any(),anyList(),anyList());
SearchParameterMap params = new SearchParameterMap();
params.add("name", new StringParam("ANAME"));
List<Long> pids = createPidSequence(10, 800);
SlowIterator iter = new SlowIterator(pids.iterator(), 1);
when(mySearchBuider.createQuery(any(), any(), any())).thenReturn(iter);
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
when(mySearchBuilder.createQuery(any(), any(), any())).thenReturn(iter);
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
when(mySearchResultDao.findWithSearchUuid(any(), any())).thenAnswer(t -> {
when(mySearchResultCacheSvc.fetchResultPids(any(), anyInt(), anyInt())).thenAnswer(t -> {
List<Long> returnedValues = iter.getReturnedValues();
Pageable page = (Pageable) t.getArguments()[1];
int offset = (int) page.getOffset();
int end = (int) (page.getOffset() + page.getPageSize());
int offset = t.getArgument(1, Integer.class);
int end = t.getArgument(2, Integer.class);
end = Math.min(end, returnedValues.size());
offset = Math.min(offset, returnedValues.size());
ourLog.info("findWithSearchUuid {} - {} out of {} values", offset, end, returnedValues.size());
return new PageImpl<>(returnedValues.subList(offset, end));
return returnedValues.subList(offset, end);
});
when(mySearchResultCacheSvc.fetchAllResultPids(any())).thenReturn(allResults);
when(mySearchCacheSvc.tryToMarkSearchAsInProgress(any())).thenAnswer(t->{
Search search = t.getArgument(0, Search.class);
assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
search.setStatus(SearchStatusEnum.LOADING);
return Optional.of(search);
});
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
@ -184,12 +195,14 @@ public class SearchCoordinatorSvcImplTest {
List<IBaseResource> resources;
when(mySearchDao.save(any())).thenAnswer(t -> {
when(mySearchCacheSvc.save(any())).thenAnswer(t -> {
Search search = (Search) t.getArguments()[0];
myCurrentSearch = search;
return search;
});
when(mySearchDao.findByUuid(any())).thenAnswer(t -> myCurrentSearch);
when(mySearchCacheSvc.fetchByUuid(any())).thenAnswer(t -> {
return Optional.ofNullable(myCurrentSearch);
});
IFhirResourceDao dao = myCallingDao;
when(myDaoRegistry.getResourceDao(any(String.class))).thenReturn(dao);
@ -199,17 +212,11 @@ public class SearchCoordinatorSvcImplTest {
assertEquals("799", resources.get(789).getIdElement().getValueAsString());
ArgumentCaptor<Search> searchCaptor = ArgumentCaptor.forClass(Search.class);
verify(mySearchDao, atLeastOnce()).save(searchCaptor.capture());
verify(mySearchResultDao, atLeastOnce()).saveAll(mySearchResultIterCaptor.capture());
List<SearchResult> allResults = new ArrayList<>();
for (Iterable<SearchResult> next : mySearchResultIterCaptor.getAllValues()) {
allResults.addAll(Lists.newArrayList(next));
}
verify(mySearchCacheSvc, atLeastOnce()).save(searchCaptor.capture());
assertEquals(790, allResults.size());
assertEquals(10, allResults.get(0).getResourcePid().longValue());
assertEquals(799, allResults.get(789).getResourcePid().longValue());
assertEquals(10, allResults.get(0).longValue());
assertEquals(799, allResults.get(789).longValue());
myExpectedNumberOfSearchBuildersCreated = 4;
}
@ -221,9 +228,9 @@ public class SearchCoordinatorSvcImplTest {
List<Long> pids = createPidSequence(10, 800);
SlowIterator iter = new SlowIterator(pids.iterator(), 2);
when(mySearchBuider.createQuery(same(params), any(), any())).thenReturn(iter);
when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNotNull(result.getUuid());
@ -249,16 +256,16 @@ public class SearchCoordinatorSvcImplTest {
List<Long> pids = createPidSequence(10, 800);
IResultIterator iter = new SlowIterator(pids.iterator(), 2);
when(mySearchBuider.createQuery(same(params), any(), any())).thenReturn(iter);
when(mySearchDao.save(any())).thenAnswer(t -> t.getArguments()[0]);
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
when(mySearchCacheSvc.save(any())).thenAnswer(t -> t.getArguments()[0]);
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNotNull(result.getUuid());
assertEquals(null, result.size());
ArgumentCaptor<Search> searchCaptor = ArgumentCaptor.forClass(Search.class);
verify(mySearchDao, atLeast(1)).save(searchCaptor.capture());
verify(mySearchCacheSvc, atLeast(1)).save(searchCaptor.capture());
Search search = searchCaptor.getValue();
assertEquals(SearchTypeEnum.SEARCH, search.getSearchType());
@ -271,7 +278,7 @@ public class SearchCoordinatorSvcImplTest {
assertEquals("10", resources.get(0).getIdElement().getValueAsString());
assertEquals("19", resources.get(9).getIdElement().getValueAsString());
when(mySearchDao.findByUuid(eq(result.getUuid()))).thenReturn(search);
when(mySearchCacheSvc.fetchByUuid(eq(result.getUuid()))).thenReturn(Optional.of(search));
/*
* Now call from a new bundle provider. This simulates a separate HTTP
@ -293,9 +300,9 @@ public class SearchCoordinatorSvcImplTest {
List<Long> pids = createPidSequence(10, 100);
SlowIterator iter = new SlowIterator(pids.iterator(), 2);
when(mySearchBuider.createQuery(same(params), any(), any())).thenReturn(iter);
when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(iter);
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNotNull(result.getUuid());
@ -324,8 +331,8 @@ public class SearchCoordinatorSvcImplTest {
search.setSearchType(SearchTypeEnum.SEARCH);
search.setResourceType("Patient");
when(mySearchDao.findByUuid(eq(uuid))).thenReturn(search);
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
when(mySearchCacheSvc.fetchByUuid(eq(uuid))).thenReturn(Optional.of(search));
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
PersistedJpaBundleProvider provider;
List<IBaseResource> resources;
@ -337,16 +344,13 @@ public class SearchCoordinatorSvcImplTest {
// ignore
}
when(mySearchResultDao.findWithSearchUuid(any(Search.class), any(Pageable.class))).thenAnswer(theInvocation -> {
Pageable page = (Pageable) theInvocation.getArguments()[1];
when(mySearchResultCacheSvc.fetchResultPids(any(Search.class), anyInt(), anyInt())).thenAnswer(theInvocation -> {
ArrayList<Long> results = new ArrayList<>();
int max = (page.getPageNumber() * page.getPageSize()) + page.getPageSize();
for (long i = page.getOffset(); i < max; i++) {
results.add(i + 10L);
}
for (long i = theInvocation.getArgument(1, Integer.class); i < theInvocation.getArgument(2, Integer.class); i++) {
results.add(i + 10L);
}
return new PageImpl<>(results);
return results;
});
search.setStatus(SearchStatusEnum.FINISHED);
}).start();
@ -377,9 +381,9 @@ public class SearchCoordinatorSvcImplTest {
params.add("name", new StringParam("ANAME"));
List<Long> pids = createPidSequence(10, 800);
when(mySearchBuider.createQuery(same(params), any(), any())).thenReturn(new ResultIterator(pids.iterator()));
when(mySearchBuilder.createQuery(same(params), any(), any())).thenReturn(new ResultIterator(pids.iterator()));
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNull(result.getUuid());
@ -398,10 +402,10 @@ public class SearchCoordinatorSvcImplTest {
params.add("name", new StringParam("ANAME"));
List<Long> pids = createPidSequence(10, 800);
when(mySearchBuider.createQuery(Mockito.same(params), any(), nullable(RequestDetails.class))).thenReturn(new ResultIterator(pids.iterator()));
when(mySearchBuilder.createQuery(Mockito.same(params), any(), nullable(RequestDetails.class))).thenReturn(new ResultIterator(pids.iterator()));
pids = createPidSequence(10, 110);
doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(eq(pids), any(Collection.class), any(List.class), anyBoolean(), nullable(RequestDetails.class));
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(eq(pids), any(Collection.class), any(List.class), anyBoolean(), nullable(RequestDetails.class));
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNull(result.getUuid());

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu2Test.java
View File

@ -20,16 +20,17 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.test.utilities.JettyUtil;
import com.google.common.collect.Lists;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.NotNull;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import javax.validation.constraints.NotNull;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
@ -38,8 +39,6 @@ import static ca.uhn.fhir.jpa.subscription.resthook.RestHookTestDstu3Test.logAll
import static org.hamcrest.CoreMatchers.containsString;
import static org.junit.Assert.*;
import ca.uhn.fhir.test.utilities.JettyUtil;
/**
* Test the rest-hook subscriptions
*/

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu3Test.java
View File

@ -17,6 +17,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.test.utilities.JettyUtil;
import com.google.common.collect.Lists;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
@ -24,11 +25,11 @@ import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.NotNull;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
import javax.validation.constraints.NotNull;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
@ -40,8 +41,6 @@ import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.*;
import ca.uhn.fhir.test.utilities.JettyUtil;
/**
* Test the rest-hook subscriptions
*/

6
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java
View File

@ -185,7 +185,11 @@ public class JdbcUtils {
DatabaseMetaData metadata;
try {
metadata = connection.getMetaData();
ResultSet indexes = metadata.getCrossReference(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theForeignTable));
String catalog = connection.getCatalog();
String schema = connection.getSchema();
String parentTable = massageIdentifier(metadata, theTableName);
String foreignTable = massageIdentifier(metadata, theForeignTable);
ResultSet indexes = metadata.getCrossReference(catalog, schema, parentTable, catalog, schema, foreignTable);
Set<String> columnNames = new HashSet<>();
while (indexes.next()) {

1
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTask.java
View File

@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
*/
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

16
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java
View File

@ -95,6 +95,13 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.POSTGRES_9_4, "oid");
setColumnType(ColumnTypeEnum.BLOB, DriverTypeEnum.MSSQL_2012, "varbinary(MAX)");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.H2_EMBEDDED, "clob");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.DERBY_EMBEDDED, "clob(100000)");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MARIADB_10_1, "longtext");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MYSQL_5_7, "longtext");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.ORACLE_12C, "clob");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.POSTGRES_9_4, "text");
setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MSSQL_2012, "varchar(MAX)");
}
public ColumnTypeEnum getColumnType() {
@ -214,8 +221,15 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
return "blob";
}
};
},
CLOB {
@Override
public String getDescriptor(Long theColumnLength) {
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
return "clob";
}
};
public abstract String getDescriptor(Long theColumnLength);

91
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropForeignKeyTask.java Normal file
View File

@ -0,0 +1,91 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
/*-
* #%L
* HAPI FHIR JPA Server - Migration
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.migrate.JdbcUtils;
import org.apache.commons.lang3.Validate;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class DropForeignKeyTask extends BaseTableTask<DropForeignKeyTask> {
private static final Logger ourLog = LoggerFactory.getLogger(DropForeignKeyTask.class);
private String myConstraintName;
private String myParentTableName;
public void setConstraintName(String theConstraintName) {
myConstraintName = theConstraintName;
}
public void setParentTableName(String theParentTableName) {
myParentTableName = theParentTableName;
}
@Override
public void validate() {
super.validate();
Validate.isTrue(isNotBlank(myConstraintName));
Validate.isTrue(isNotBlank(myParentTableName));
}
@Override
public void execute() throws SQLException {
Set<String> existing = JdbcUtils.getForeignKeys(getConnectionProperties(), myParentTableName, getTableName());
if (!existing.contains(myConstraintName)) {
ourLog.info("Don't have constraint named {} - No action performed", myConstraintName);
return;
}
String sql = null;
String sql2 = null;
switch (getDriverType()) {
case MYSQL_5_7:
// Lousy MYQL....
sql = "alter table " + getTableName() + " drop constraint " + myConstraintName;
sql2 = "alter table " + getTableName() + " drop index " + myConstraintName;
break;
case MARIADB_10_1:
case POSTGRES_9_4:
case DERBY_EMBEDDED:
case H2_EMBEDDED:
case ORACLE_12C:
case MSSQL_2012:
sql = "alter table " + getTableName() + " drop constraint " + myConstraintName;
break;
default:
throw new IllegalStateException();
}
executeSql(getTableName(), sql);
if (isNotBlank(sql2)) {
executeSql(getTableName(), sql2);
}
}
}

101
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIdGeneratorTask.java Normal file
View File

@ -0,0 +1,101 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
/*-
* #%L
* HAPI FHIR JPA Server - Migration
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.migrate.JdbcUtils;
import org.apache.commons.lang3.Validate;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
import java.util.Set;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class DropIdGeneratorTask extends BaseTask<DropIdGeneratorTask> {
private static final Logger ourLog = LoggerFactory.getLogger(DropIdGeneratorTask.class);
private final String myGeneratorName;
public DropIdGeneratorTask(String theGeneratorName) {
myGeneratorName = theGeneratorName;
}
@Override
public void validate() {
Validate.notBlank(myGeneratorName);
}
@Override
public void execute() throws SQLException {
Set<String> tableNames = JdbcUtils.getTableNames(getConnectionProperties());
String sql = null;
switch (getDriverType()) {
case MARIADB_10_1:
case MYSQL_5_7:
// These require a separate table
if (tableNames.contains(myGeneratorName)) {
String initSql = "delete from " + myGeneratorName;
executeSql(myGeneratorName, initSql);
String creationSql = "drop table " + myGeneratorName;
executeSql(myGeneratorName, creationSql);
}
break;
case DERBY_EMBEDDED:
case H2_EMBEDDED:
sql = "drop sequence " + myGeneratorName;
break;
case POSTGRES_9_4:
sql = "drop sequence " + myGeneratorName;
break;
case ORACLE_12C:
sql = "drop sequence " + myGeneratorName;
break;
case MSSQL_2012:
sql = "drop sequence " + myGeneratorName;
break;
default:
throw new IllegalStateException();
}
if (isNotBlank(sql)) {
Set<String> sequenceNames =
JdbcUtils.getSequenceNames(getConnectionProperties())
.stream()
.map(String::toLowerCase)
.collect(Collectors.toSet());
ourLog.debug("Currently have sequences: {}", sequenceNames);
if (!sequenceNames.contains(myGeneratorName.toLowerCase())) {
ourLog.info("Sequence {} does not exist - No action performed", myGeneratorName);
return;
}
executeSql(myGeneratorName, sql);
}
}
}

99
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -87,12 +87,19 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addForeignKey("FK_TRM_VSCD_VS_PID")
.toColumn("VALUESET_PID")
.references("TRM_VALUESET", "PID");
// Drop HFJ_SEARCH_RESULT foreign keys
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_RES", "HFJ_RESOURCE");
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_SEARCH", "HFJ_SEARCH");
// TermValueSet
version.startSectionWithMessage("Processing table: TRM_VALUESET");
Builder.BuilderWithTableName termValueSetTable = version.onTable("TRM_VALUESET");
termValueSetTable.addColumn("TOTAL_CONCEPTS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable.addColumn("TOTAL_CONCEPT_DESIGNATIONS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable
.dropIndex("IDX_VALUESET_EXP_STATUS");
version.dropIdGenerator("SEQ_SEARCHPARM_ID");
// TermValueSetConcept
version.startSectionWithMessage("Processing table: TRM_VALUESET_CONCEPT");
@ -124,22 +131,54 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.renameColumn("myConceptMapUrl", "CONCEPT_MAP_URL", false, true)
.renameColumn("mySourceValueSet", "SOURCE_VS", false, true)
.renameColumn("myTargetValueSet", "TARGET_VS", false, true);
version.onTable("TRM_CONCEPT_MAP_GROUP")
.modifyColumn("CONCEPT_MAP_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GROUP")
.modifyColumn("SOURCE_VERSION").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GROUP")
.modifyColumn("SOURCE_VS").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GROUP")
.modifyColumn("TARGET_VERSION").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GROUP")
.modifyColumn("TARGET_VS").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
.renameColumn("myConceptMapUrl", "CONCEPT_MAP_URL", false, true)
.renameColumn("mySystem", "SYSTEM_URL", false, true)
.renameColumn("mySystemVersion", "SYSTEM_VERSION", false, true)
.renameColumn("myValueSet", "VALUESET_URL", false, true);
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
.modifyColumn("CONCEPT_MAP_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
.modifyColumn("SOURCE_CODE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 500);
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
.modifyColumn("SYSTEM_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
.modifyColumn("SYSTEM_VERSION").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
.modifyColumn("VALUESET_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.renameColumn("myConceptMapUrl", "CONCEPT_MAP_URL", false, true)
.renameColumn("mySystem", "SYSTEM_URL", false, true)
.renameColumn("mySystemVersion", "SYSTEM_VERSION", false, true)
.renameColumn("myValueSet", "VALUESET_URL", false, true);
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.modifyColumn("CONCEPT_MAP_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.modifyColumn("SYSTEM_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.modifyColumn("SYSTEM_VERSION").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.modifyColumn("TARGET_CODE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 500);
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.modifyColumn("VALUESET_URL").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CONCEPT")
.renameColumn("CODE", "CODEVAL", false, true);
// TermValueSet
version.startSectionWithMessage("Processing table: TRM_VALUESET");
version.addIdGenerator("SEQ_VALUESET_PID");
@ -159,6 +198,8 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
version.onTable("TRM_VALUESET")
.renameColumn("NAME", "VSNAME", true, true);
version.onTable("TRM_VALUESET")
.modifyColumn("RES_ID").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
Builder.BuilderWithTableName termValueSetTableChange = version.onTable("TRM_VALUESET");
termValueSetTableChange.addColumn("EXPANSION_STATUS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermValueSet.MAX_EXPANSION_STATUS_LENGTH);
@ -215,6 +256,47 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
version.startSectionWithMessage("Processing table: TRM_CODESYSTEM_VER");
Builder.BuilderWithTableName termCodeSystemVersionTable = version.onTable("TRM_CODESYSTEM_VER");
termCodeSystemVersionTable.addColumn("CS_DISPLAY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermCodeSystemVersion.MAX_VERSION_LENGTH);
// ResourceReindexJobEntry
version.addIdGenerator("SEQ_RES_REINDEX_JOB");
Builder.BuilderAddTableByColumns reindex = version.addTableByColumns("HFJ_RES_REINDEX_JOB", "PID");
reindex.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
reindex.addColumn("RES_TYPE").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, Constants.MAX_RESOURCE_NAME_LENGTH);
reindex.addColumn("UPDATE_THRESHOLD_HIGH").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP);
reindex.addColumn("JOB_DELETED").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.BOOLEAN);
reindex.addColumn("UPDATE_THRESHOLD_LOW").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP);
reindex.addColumn("SUSPENDED_UNTIL").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP);
reindex.addColumn("REINDEX_COUNT").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.INT);
// Search
version.onTable("HFJ_SEARCH")
.addColumn("SEARCH_DELETED").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.BOOLEAN);
version.onTable("HFJ_SEARCH")
.modifyColumn("SEARCH_LAST_RETURNED").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP);
version.onTable("HFJ_SEARCH")
.addColumn("SEARCH_PARAM_MAP").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.BLOB);
version.onTable("HFJ_SEARCH")
.modifyColumn("SEARCH_UUID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, Search.UUID_COLUMN_LENGTH);
version.onTable("HFJ_SEARCH_PARM").dropThisTable();
version.onTable("HFJ_SPIDX_COORDS").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_DATE").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_STRING").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_STRING").addColumn("HASH_IDENTITY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_STRING").addIndex("IDX_SP_STRING_HASH_IDENT").unique(false).withColumns("HASH_IDENTITY");
version.onTable("HFJ_SPIDX_COORDS").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_QUANTITY").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_QUANTITY").dropColumn("HASH_UNITS_AND_VALPREFIX");
version.onTable("HFJ_SPIDX_QUANTITY").dropColumn("HASH_VALPREFIX");
version.onTable("HFJ_SPIDX_NUMBER").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_TOKEN").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_URI").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_URI").modifyColumn("SP_URI").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 254);
version.onTable("TRM_CODESYSTEM").modifyColumn("CODE_SYSTEM_URI").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CODESYSTEM").modifyColumn("CS_NAME").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CODESYSTEM_VER").modifyColumn("CS_VERSION_ID").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
}
@ -245,6 +327,14 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addSql(DriverTypeEnum.MYSQL_5_7, " create table HFJ_RES_REINDEX_JOB (PID bigint not null, JOB_DELETED bit not null, RES_TYPE varchar(255), SUSPENDED_UNTIL datetime(6), UPDATE_THRESHOLD_HIGH datetime(6) not null, UPDATE_THRESHOLD_LOW datetime(6), primary key (PID))")
.addSql(DriverTypeEnum.ORACLE_12C, "create table HFJ_RES_REINDEX_JOB (PID number(19,0) not null, JOB_DELETED number(1,0) not null, RES_TYPE varchar2(255 char), SUSPENDED_UNTIL timestamp, UPDATE_THRESHOLD_HIGH timestamp not null, UPDATE_THRESHOLD_LOW timestamp, primary key (PID))");
version.onTable("TRM_CONCEPT_DESIG").addColumn("CS_VER_PID").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("TRM_CONCEPT_DESIG").addForeignKey("FK_CONCEPTDESIG_CSV").toColumn("CS_VER_PID").references("TRM_CODESYSTEM_VER", "PID");
version.onTable("TRM_CONCEPT_PROPERTY").addColumn("CS_VER_PID").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("TRM_CONCEPT_PROPERTY").addForeignKey("FK_CONCEPTPROP_CSV").toColumn("CS_VER_PID").references("TRM_CODESYSTEM_VER", "PID");
version.onTable("TRM_CONCEPT").addColumn("PARENT_PIDS").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.CLOB);
}
private void init350() {
@ -299,6 +389,8 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addIndex("IDX_SP_DATE_HASH")
.unique(false)
.withColumns("HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH");
spidxDate
.dropIndex("IDX_SP_DATE");
spidxDate
.addTask(new CalculateHashesTask()
.setColumnName("HASH_IDENTITY")
@ -531,6 +623,9 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_DESIG");
version
.addTableRawSql("TRM_CONCEPT_DESIG")
.addSql(DriverTypeEnum.H2_EMBEDDED, "create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
.addSql(DriverTypeEnum.H2_EMBEDDED, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
.addSql(DriverTypeEnum.H2_EMBEDDED, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
@ -658,6 +753,10 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID bigint not null, TARGET_CODE varchar(500) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID bigint not null, primary key (PID))")
.addSql(DriverTypeEnum.MSSQL_2012, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT");
version.onTable("HFJ_IDX_CMP_STRING_UNIQ").modifyColumn("IDX_STRING").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
}
private Boolean columnToBoolean(Object theValue) {

18
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/BaseMigrationTasks.java
View File

@ -117,6 +117,11 @@ public class BaseMigrationTasks<T extends Enum> {
addTask(task);
}
public void dropIdGenerator(String theIdGeneratorName) {
DropIdGeneratorTask task = new DropIdGeneratorTask(theIdGeneratorName);
addTask(task);
}
public class BuilderAddTableRawSql {
private final AddTableRawSqlTask myTask;
@ -241,6 +246,19 @@ public class BaseMigrationTasks<T extends Enum> {
return this;
}
/**
*
* @param theFkName the name of the foreign key
* @param theParentTableName the name of the table that exports the foreign key
*/
public void dropForeignKey(String theFkName, String theParentTableName) {
DropForeignKeyTask task = new DropForeignKeyTask();
task.setConstraintName(theFkName);
task.setTableName(getTableName());
task.setParentTableName(theParentTableName);
addTask(task);
}
public class BuilderAddIndexWithName {
private final String myIndexName;

4
hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTest.java
View File

@ -1,12 +1,12 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import com.google.common.collect.Lists;
import org.junit.Test;
import java.sql.SQLException;
import static org.hamcrest.Matchers.*;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.hasItem;
import static org.junit.Assert.assertThat;
public class AddIndexTest extends BaseTest {

38
hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/DropForeignKeyTaskTest.java Normal file
View File

@ -0,0 +1,38 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import org.junit.Test;
import java.sql.SQLException;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.collection.IsCollectionWithSize.hasSize;
import static org.junit.Assert.assertThat;
public class DropForeignKeyTaskTest extends BaseTest {
@Test
public void testDropForeignKey() throws SQLException {
executeSql("create table PARENT (PID bigint not null, TEXTCOL varchar(255), primary key (PID))");
executeSql("create table CHILD (PID bigint not null, PARENTREF bigint)");
executeSql("alter table CHILD add constraint FK_MOM foreign key (PARENTREF) references PARENT(PID)");
assertThat(JdbcUtils.getForeignKeys(getConnectionProperties(), "PARENT", "CHILD"), hasSize(1));
DropForeignKeyTask task = new DropForeignKeyTask();
task.setTableName("CHILD");
task.setParentTableName("PARENT");
task.setConstraintName("FK_MOM");
getMigrator().addTask(task);
getMigrator().migrate();
assertThat(JdbcUtils.getForeignKeys(getConnectionProperties(), "PARENT", "CHILD"), empty());
// Make sure additional calls don't crash
getMigrator().migrate();
getMigrator().migrate();
}
}

41
hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIdGeneratorTaskTest.java Normal file
View File

@ -0,0 +1,41 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import ca.uhn.fhir.jpa.migrate.tasks.api.BaseMigrationTasks;
import ca.uhn.fhir.util.VersionEnum;
import org.junit.Test;
import java.sql.SQLException;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.assertThat;
public class DropIdGeneratorTaskTest extends BaseTest {
@Test
public void testAddIdGenerator() throws SQLException {
executeSql("create sequence SEQ_FOO start with 1 increment by 50");
assertThat(JdbcUtils.getSequenceNames(getConnectionProperties()), containsInAnyOrder("SEQ_FOO"));
MyMigrationTasks migrator = new MyMigrationTasks();
getMigrator().addTasks(migrator.getTasks(VersionEnum.V3_3_0, VersionEnum.V3_6_0));
getMigrator().migrate();
assertThat(JdbcUtils.getSequenceNames(getConnectionProperties()), empty());
}
private static class MyMigrationTasks extends BaseMigrationTasks<VersionEnum> {
public MyMigrationTasks() {
Builder v = forVersion(VersionEnum.V3_5_0);
v.dropIdGenerator("SEQ_FOO");
}
}
}

5
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
View File

@ -877,6 +877,11 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
return false;
}
@Override
public ValueSet resolveValueSet(Object appContext, String url) {
return null;
}
}
private static <T extends Enum<?>> String extractSystem(Enumeration<T> theBoundCode) {

2
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
View File

@ -21,12 +21,10 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
*/
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.util.StringNormalizer;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.annotations.VisibleForTesting;

5
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/module/subscriber/SubscriptionMatchingSubscriber.java
View File

@ -18,7 +18,10 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.messaging.*;
import org.springframework.messaging.Message;
import org.springframework.messaging.MessageChannel;
import org.springframework.messaging.MessageHandler;
import org.springframework.messaging.MessagingException;
import org.springframework.stereotype.Service;
import java.util.Collection;

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
View File

@ -848,7 +848,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
@SuppressWarnings("WeakerAccess")
protected void handleRequest(RequestTypeEnum theRequestType, HttpServletRequest theRequest, HttpServletResponse theResponse) throws ServletException, IOException {
String fhirServerBase;
ServletRequestDetails requestDetails = new ServletRequestDetails(getInterceptorService());
ServletRequestDetails requestDetails = newRequestDetails();
requestDetails.setServer(this);
requestDetails.setRequestType(theRequestType);
requestDetails.setServletRequest(theRequest);
@ -1095,6 +1095,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
}
}
protected ServletRequestDetails newRequestDetails() {
return new ServletRequestDetails(getInterceptorService());
}
protected void addRequestIdToResponse(ServletRequestDetails theRequestDetails, String theRequestId) {
theRequestDetails.getResponse().addHeader(Constants.HEADER_REQUEST_ID, theRequestId);
}

12
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ResourceParameter.java
View File

@ -157,9 +157,6 @@ public class ResourceParameter implements IParameter {
}
}
if (isBlank(ctValue)) {
/*
* If the client didn't send a content type, try to guess
*/
String body;
try {
body = IOUtils.toString(requestReader);
@ -170,12 +167,9 @@ public class ResourceParameter implements IParameter {
if (isBlank(body)) {
return null;
}
encoding = EncodingEnum.detectEncodingNoDefault(body);
if (encoding == null) {
String msg = ctx.getLocalizer().getMessage(ResourceParameter.class, "noContentTypeInRequest", restOperationType);
throw new InvalidRequestException(msg);
}
requestReader = new InputStreamReader(new ByteArrayInputStream(theRequest.loadRequestContents()), charset);
String msg = ctx.getLocalizer().getMessage(ResourceParameter.class, "noContentTypeInRequest", restOperationType);
throw new InvalidRequestException(msg);
} else {
String msg = ctx.getLocalizer().getMessage(ResourceParameter.class, "invalidContentTypeInRequest", ctValue, restOperationType);
throw new InvalidRequestException(msg);

12
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/HapiWorkerContext.java
View File

@ -336,6 +336,18 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
expandedValueSet = new ValueSetExpansionOutcome(expansion);
}
/*
* We'll just accept all mimetypes, since this is pretty much impossible to exhaustively
* validate.
*/
if (theVs != null && "http://hl7.org/fhir/ValueSet/mimetypes".equals(theVs.getUrl())) {
ConceptDefinitionComponent definition = new ConceptDefinitionComponent();
definition.setCode(wantCode);
definition.setDisplay(wantCode);
ValidationResult retVal = new ValidationResult(definition);
return retVal;
}
if (expandedValueSet == null) {
expandedValueSet = expand(theVs, null);
}

5
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/HapiWorkerContext.java
View File

@ -389,6 +389,11 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
throw new UnsupportedOperationException();
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public List<String> getTypeNames() {
throw new UnsupportedOperationException();

17
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/CreateR4Test.java
View File

@ -77,6 +77,23 @@ public class CreateR4Test {
}
@Test
public void testCreateFailsIfNoContentTypeProvided() throws Exception {
HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient");
httpPost.setEntity(new StringEntity("{\"resourceType\":\"Patient\", \"id\":\"999\", \"status\":\"active\"}", (ContentType) null));
try (CloseableHttpResponse status = ourClient.execute(httpPost)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info("Response was:\n{}", responseContent);
assertEquals(400, status.getStatusLine().getStatusCode());
assertThat(responseContent, containsString("No Content-Type header was provided in the request. This is required for \\\"CREATE\\\" operation"));
}
}
/**
* #472
*/

2
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/OperationGenericServer2R4Test.java
View File

@ -232,9 +232,9 @@ public class OperationGenericServer2R4Test {
HttpGet httpPost = new HttpGet("http://localhost:" + myPort + "/Patient/123/$OP_INSTANCE");
try (CloseableHttpResponse status = ourClient.execute(httpPost)) {
assertEquals(200, status.getStatusLine().getStatusCode());
String response = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertEquals(200, status.getStatusLine().getStatusCode());
status.getEntity().getContent().close();
assertEquals("123", ourLastId.getIdPart());

6
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/GraphQLEngineTest.java
View File

@ -66,7 +66,8 @@ public class GraphQLEngineTest {
engine.setGraphQL(Parser.parse("{valueQuantity{value,unit}}"));
engine.execute();
ObjectValue output = engine.getOutput();
GraphQLResponse output = engine.getOutput();
output.setWriteWrapper(false);
StringBuilder outputBuilder = new StringBuilder();
output.write(outputBuilder, 0, "\n");
@ -100,7 +101,8 @@ public class GraphQLEngineTest {
engine.setServices(createStorageServices());
engine.execute();
ObjectValue output = engine.getOutput();
GraphQLResponse output = engine.getOutput();
output.setWriteWrapper(false);
StringBuilder outputBuilder = new StringBuilder();
output.write(outputBuilder, 0, "\n");

5
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/HapiWorkerContext.java
View File

@ -438,4 +438,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
throw new UnsupportedOperationException();
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
}

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -339,6 +339,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
throw new UnsupportedOperationException();
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p) throws FHIRException {
// nothing yet

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidator.java
View File

@ -522,6 +522,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public Parameters getExpansionParameters() {
return myExpansionProfile;

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/FhirInstanceValidator.java
View File

@ -669,6 +669,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
return convertValidationResult(result);
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
}
private static class ResourceKey {

6
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/SnapshotGeneratingValidationSupport.java
View File

@ -145,6 +145,12 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
public boolean prependLinks() {
return false;
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
}
}

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/FhirInstanceValidator.java
View File

@ -282,6 +282,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
// nothing yet
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public org.hl7.fhir.r5.model.Parameters getExpansionParameters() {
return myExpansionProfile;

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/SnapshotGeneratingValidationSupport.java
View File

@ -131,6 +131,11 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
return null;
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public BindingResolution resolveBinding(StructureDefinition def, String url, String path) throws FHIRException {
return null;

2
pom.xml
View File

@ -562,7 +562,7 @@
<properties>
<fhir_core_version>4.0.2-SNAPSHOT</fhir_core_version>
<fhir_core_version>4.0.8-SNAPSHOT</fhir_core_version>
<ucum_version>1.0.2</ucum_version>
<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->

17
src/changes/changes.xml
View File

@ -73,9 +73,13 @@
The informational message returned in an OperationOutcome when a delete failed due to cascades not being enabled
contained an incorrect example. This has been corrected.
</action>
<action type="change">
Two foreign keys have been dropped from the HFJ_SEARCH_RESULT table used by the FHIR search query cache. These
constraints did not add value and caused unneccessary contention when used under high load.
</action>
<action type="change">
An inefficient regex expression in UrlUtil was replaced with a much more efficient hand-written
checker. This regex was causing a noticable performance drop when feeding large numbers of transactions
checker. This regex was causing a noticable performance drop when feeding large numbers of transactions
into the JPA server at the same time (i.e. when loading Synthea data).
</action>
<action type="fix">
@ -106,6 +110,17 @@
A note has been added to the downloads page explaning the removal of the hapi-fhir-utilities
module. Thanks to Andrew Fitzgerald for the PR!
</action>
<action type="change">
REST servers will no longer try to guess the content type for HTTP requests where a body
is provided but no Content-Type header is included. These requests are invalid, and will now
result in an HTTP 400. This change corrects an error where some interceptors (notably
the RequestValidatingInterceptor, but not including any HAPI FHIR security interceptors)
could be bypassed if a Content Type was not included.
</action>
<action type="fix">
The GraphQL provider did not wrap the respone in a "data" element as described in the FHIR
specification. This has been corrected.
</action>
</release>
<release version="4.0.1" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix">