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Fix indexing bug

This commit is contained in:
James Agnew 2018-12-04 18:50:49 -05:00
parent d9ce0ebf7c
commit 1d3bcd9e8f
5 changed files with 35 additions and 20 deletions
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12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -876,6 +876,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public T read(IIdType theId, RequestDetails theRequestDetails) {
return read(theId, theRequestDetails, false);
}
@Override
public T read(IIdType theId, RequestDetails theRequestDetails, boolean theDeletedOk) {
validateResourceTypeAndThrowIllegalArgumentException(theId);
// Notify interceptors
@ -891,10 +896,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
T retVal = toResource(myResourceType, entity, null, false);
if (entity.getDeleted() != null) {
throw new ResourceGoneException("Resource was deleted at " + new InstantType(entity.getDeleted()).getValueAsString());
if (theForHistory == false) {
if (entity.getDeleted() != null) {
throw new ResourceGoneException("Resource was deleted at " + new InstantType(entity.getDeleted()).getValueAsString());
}
}
ourLog.debug("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
return retVal;
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDao.java
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@ -171,6 +171,12 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
*/
T read(IIdType theId, RequestDetails theRequestDetails);
/**
* Should deleted resources be returned successfully. This should be false for
* a normal FHIR read.
*/
T read(IIdType theId, RequestDetails theRequestDetails, boolean theDeletedOk);
BaseHasResource readEntity(IIdType theId);
/**

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
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@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
@ -460,7 +461,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceTable.getResourceType());
long expectedVersion = resourceTable.getVersion();
IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless());
IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless(), null,true);
if (resource == null) {
throw new InternalErrorException("Could not find resource version " + resourceTable.getIdDt().toUnqualified().getValue() + " in database");
}

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

@ -237,7 +237,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
runInTransaction(() -> {
Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
assertTrue(tableOpt.isPresent());
assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED, tableOpt.get().getIndexStatus().longValue());
assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, tableOpt.get().getIndexStatus().longValue());
assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), not(greaterThan(0)));
});

32
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImplTest.java
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@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.junit.Before;
@ -197,22 +198,22 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
"Patient"
};
List<IBaseResource> resources = Arrays.asList(
new Patient().setId("Patient/0"),
new Patient().setId("Patient/1"),
new Patient().setId("Patient/2"),
new Patient().setId("Patient/3")
new Patient().setId("Patient/0/_history/1"),
new Patient().setId("Patient/1/_history/1"),
new Patient().setId("Patient/2/_history/1"),
new Patient().setId("Patient/3/_history/1")
);
mockWhenResourceTableFindById(updatedTimes, resourceTypes);
when(myDaoRegistry.getResourceDao(eq("Patient"))).thenReturn(myResourceDao);
when(myDaoRegistry.getResourceDao(eq(Patient.class))).thenReturn(myResourceDao);
when(myDaoRegistry.getResourceDao(eq("Observation"))).thenReturn(myResourceDao);
when(myDaoRegistry.getResourceDao(eq(Observation.class))).thenReturn(myResourceDao);
when(myResourceDao.toResource(any(), anyBoolean())).thenAnswer(t -> {
ResourceTable table = (ResourceTable) t.getArguments()[0];
Long id = table.getId();
return resources.get(id.intValue());
when(myResourceDao.read(any())).thenAnswer(t->{
IIdType id = (IIdType) t.getArguments()[0];
return resources.get(id.getIdPartAsLong().intValue());
});
int count = mySvc.forceReindexingPass();
assertEquals(4, count);
@ -258,20 +259,19 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
"Observation"
};
List<IBaseResource> resources = Arrays.asList(
new Patient().setId("Patient/0"),
new Patient().setId("Patient/1"),
new Observation().setId("Observation/2"),
new Observation().setId("Observation/3")
new Patient().setId("Patient/0/_history/1"),
new Patient().setId("Patient/1/_history/1"),
new Observation().setId("Observation/2/_history/1"),
new Observation().setId("Observation/3/_history/1")
);
mockWhenResourceTableFindById(updatedTimes, resourceTypes);
when(myDaoRegistry.getResourceDao(eq("Patient"))).thenReturn(myResourceDao);
when(myDaoRegistry.getResourceDao(eq(Patient.class))).thenReturn(myResourceDao);
when(myDaoRegistry.getResourceDao(eq("Observation"))).thenReturn(myResourceDao);
when(myDaoRegistry.getResourceDao(eq(Observation.class))).thenReturn(myResourceDao);
when(myResourceDao.toResource(any(), anyBoolean())).thenAnswer(t -> {
ResourceTable table = (ResourceTable) t.getArguments()[0];
Long id = table.getId();
return resources.get(id.intValue());
when(myResourceDao.read(any())).thenAnswer(t->{
IIdType id = (IIdType) t.getArguments()[0];
return resources.get(id.getIdPartAsLong().intValue());
});
}