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Fix a crash when reindexing deleted resources

This commit is contained in:
James Agnew 2018-07-02 09:17:30 -04:00
parent 6d83edabb6
commit 3b794a4f39
7 changed files with 77 additions and 19 deletions
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5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -1772,8 +1772,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
Validate.notNull(theEntity);
Validate.isTrue(theDeletedTimestampOrNull != null || theResource != null, "Must have either a resource[{}] or a deleted timestamp[{}] for resource PID[{}]", theDeletedTimestampOrNull != null, theResource != null, theEntity.getId());
ourLog.debug("Starting entity update");
/*
* This should be the very first thing..
*/
@ -1863,6 +1867,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
theEntity.setNarrativeTextParsedIntoWords(null);
theEntity.setContentTextParsedIntoWords(null);
theEntity.setHashSha256(null);
theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
changed = populateResourceIntoEntity(theRequest, theResource, theEntity, true);
} else {

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -927,11 +927,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public void reindex(T theResource, ResourceTable theEntity) {
ourLog.debug("Indexing resource {} - PID {}", theResource.getIdElement().getValue(), theEntity.getId());
ourLog.debug("Indexing resource {} - PID {}", theEntity.getIdDt().getValue(), theEntity.getId());
if (theResource != null) {
CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
updateEntity(null, theResource, theEntity, null, true, false, theEntity.getUpdatedDate(), true, false);
}
updateEntity(null, theResource, theEntity, theEntity.getDeleted(), true, false, theEntity.getUpdatedDate(), true, false);
if (theResource != null) {
CURRENTLY_REINDEXING.put(theResource, null);
}
}
@Override
public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {
@ -1062,6 +1066,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
mySecondaryPrimaryKeyParamName = theSecondaryPrimaryKeyParamName;
}
@PostConstruct
public void start() {
ourLog.debug("Starting resource DAO for type: {}", getResourceName());
}
protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) {
MT retVal;
try {
@ -1333,9 +1342,4 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
@PostConstruct
public void start() {
ourLog.debug("Starting resource DAO for type: {}", getResourceName());
}
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceIndexedSearchParamStringDao.java
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@ -23,7 +23,12 @@ package ca.uhn.fhir.jpa.dao.data;
import org.springframework.data.jpa.repository.JpaRepository;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
public interface IResourceIndexedSearchParamStringDao extends JpaRepository<ResourceIndexedSearchParamString, Long> {
// nothing yet
@Query("select count(*) from ResourceIndexedSearchParamString t WHERE t.myResourcePid = :resid")
int countForResourceId(@Param("resid") Long theResourcePid);
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceIndexedSearchParamTokenDao.java
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@ -20,10 +20,14 @@ package ca.uhn.fhir.jpa.dao.data;
* #L%
*/
import org.springframework.data.jpa.repository.JpaRepository;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
public interface IResourceIndexedSearchParamTokenDao extends JpaRepository<ResourceIndexedSearchParamToken, Long> {
// nothing yet
@Query("select count(*) from ResourceIndexedSearchParamToken t WHERE t.myResourcePid = :resid")
int countForResourceId(@Param("resid") Long theResourcePid);
}

41
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
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@ -1,10 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
@ -152,6 +149,42 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
return retVal;
}
@Test
public void testDeletedResourcesAreReindexed() {
myDaoConfig.setSchedulingDisabled(true);
Patient pt1 = new Patient();
pt1.setActive(true);
pt1.addName().setFamily("FAM");
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
runInTransaction(()->{
assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), greaterThan(0));
});
runInTransaction(()->{
Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
assertTrue(tableOpt.isPresent());
ResourceTable table = tableOpt.get();
table.setIndexStatus(null);
table.setDeleted(new Date());
});
mySystemDao.performReindexingPass(1000);
mySystemDao.performReindexingPass(1000);
runInTransaction(()->{
Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
assertTrue(tableOpt.isPresent());
assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, tableOpt.get().getIndexStatus().longValue());
assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), not(greaterThan(0)));
});
}
@Test
public void testCantSearchForDeletedResourceByLanguageOrTag() {
String methodName = "testCantSearchForDeletedResourceByLanguageOrTag";

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
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@ -1,9 +1,11 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.SearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.util.JpaConstants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
@ -27,6 +29,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import static org.hamcrest.Matchers.*;

4
src/changes/changes.xml
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@ -134,6 +134,10 @@
A crash was fixed when deleting a ConceptMap resource in the
JPA server. This crash was a regression in HAPI FHIR 3.4.0.
</action>
<action type="fix">
A crash in the JPA server when performing a manual reindex of a deleted resource
was fixed.
</action>
</release>
<release version="3.4.0" date="2018-05-28">
<action type="add">