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hapi-fhir
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Merge branch 'master' into npe_fix

This commit is contained in:
Jari Maijenburg 2021-09-07 17:36:05 +02:00 committed by GitHub
parent cdb7ffb0d3 41e8dd93f0
commit d3d7c6e97e
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2 changed files with 94 additions and 92 deletions
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175
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -618,6 +618,48 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
skipUpdatingTags |= myConfig.getTagStorageMode() == DaoConfig.TagStorageModeEnum.INLINE; skipUpdatingTags |= myConfig.getTagStorageMode() == DaoConfig.TagStorageModeEnum.INLINE;
if (!skipUpdatingTags) { if (!skipUpdatingTags) {
changed |= updateTags(theTransactionDetails, theRequest, theResource, theEntity);
}
} else {
theEntity.setHashSha256(null);
bytes = null;
encoding = ResourceEncodingEnum.DEL;
}
if (thePerformIndexing && !changed) {
if (theEntity.getId() == null) {
changed = true;
} else if (myConfig.isMassIngestionMode()) {
// Don't check existing - We'll rely on the SHA256 hash only
} else if (theEntity.getVersion() == 1L && theEntity.getCurrentVersionEntity() == null) {
// No previous version if this is the first version
} else {
ResourceHistoryTable currentHistoryVersion = theEntity.getCurrentVersionEntity();
if (currentHistoryVersion == null) {
currentHistoryVersion = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), theEntity.getVersion());
}
if (currentHistoryVersion == null || currentHistoryVersion.getResource() == null) {
changed = true;
} else {
changed = !Arrays.equals(currentHistoryVersion.getResource(), bytes);
}
}
}
EncodedResource retVal = new EncodedResource();
retVal.setEncoding(encoding);
retVal.setResource(bytes);
retVal.setChanged(changed);
return retVal;
}
private boolean updateTags(TransactionDetails theTransactionDetails, RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity) {
Set<ResourceTag> allDefs = new HashSet<>(); Set<ResourceTag> allDefs = new HashSet<>();
Set<ResourceTag> allTagsOld = getAllTagDefinitions(theEntity); Set<ResourceTag> allTagsOld = getAllTagDefinitions(theEntity);
@ -657,48 +699,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}); });
if (!allTagsOld.equals(allTagsNew)) {
changed = true;
}
theEntity.setHasTags(!allTagsNew.isEmpty()); theEntity.setHasTags(!allTagsNew.isEmpty());
} return !allTagsOld.equals(allTagsNew);
} else {
theEntity.setHashSha256(null);
bytes = null;
encoding = ResourceEncodingEnum.DEL;
}
if (thePerformIndexing && changed == false) {
if (theEntity.getId() == null) {
changed = true;
} else if (myConfig.isMassIngestionMode()) {
// Don't check existing - We'll rely on the SHA256 hash only
} else if (theEntity.getVersion() == 1L && theEntity.getCurrentVersionEntity() == null) {
// No previous version if this is the first version
} else {
ResourceHistoryTable currentHistoryVersion = theEntity.getCurrentVersionEntity();
if (currentHistoryVersion == null) {
currentHistoryVersion = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), theEntity.getVersion());
}
if (currentHistoryVersion == null || currentHistoryVersion.getResource() == null) {
changed = true;
} else {
changed = !Arrays.equals(currentHistoryVersion.getResource(), bytes);
}
}
}
EncodedResource retVal = new EncodedResource();
retVal.setEncoding(encoding);
retVal.setResource(bytes);
retVal.setChanged(changed);
return retVal;
} }
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
@ -1288,52 +1290,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
postUpdate(entity, (T) theResource); postUpdate(entity, (T) theResource);
} }
/*
* Create history entry
*/
if (theCreateNewHistoryEntry) { if (theCreateNewHistoryEntry) {
boolean versionedTags = getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.VERSIONED; createHistoryEntry(theRequest, theResource, entity, changed);
final ResourceHistoryTable historyEntry = entity.toHistory(versionedTags);
historyEntry.setEncoding(changed.getEncoding());
historyEntry.setResource(changed.getResource());
ourLog.debug("Saving history entry {}", historyEntry.getIdDt());
myResourceHistoryTableDao.save(historyEntry);
// Save resource source
String source = null;
String requestId = theRequest != null ? theRequest.getRequestId() : null;
if (theResource != null) {
if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
IBaseMetaType meta = theResource.getMeta();
source = MetaUtil.getSource(myContext, meta);
}
if (myContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
source = ((IBaseHasExtensions) theResource.getMeta())
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXT_META_SOURCE.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()).getValueAsString())
.findFirst()
.orElse(null);
}
}
boolean haveSource = isNotBlank(source) && myConfig.getStoreMetaSourceInformation().isStoreSourceUri();
boolean haveRequestId = isNotBlank(requestId) && myConfig.getStoreMetaSourceInformation().isStoreRequestId();
if (haveSource || haveRequestId) {
ResourceHistoryProvenanceEntity provenance = new ResourceHistoryProvenanceEntity();
provenance.setResourceHistoryTable(historyEntry);
provenance.setResourceTable(entity);
provenance.setPartitionId(entity.getPartitionId());
if (haveRequestId) {
provenance.setRequestId(left(requestId, Constants.REQUEST_ID_LENGTH));
}
if (haveSource) {
provenance.setSourceUri(source);
}
myEntityManager.persist(provenance);
}
} }
/* /*
@ -1415,6 +1373,51 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
return entity; return entity;
} }
private void createHistoryEntry(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, EncodedResource theChanged) {
boolean versionedTags = getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.VERSIONED;
final ResourceHistoryTable historyEntry = theEntity.toHistory(versionedTags);
historyEntry.setEncoding(theChanged.getEncoding());
historyEntry.setResource(theChanged.getResource());
ourLog.debug("Saving history entry {}", historyEntry.getIdDt());
myResourceHistoryTableDao.save(historyEntry);
// Save resource source
String source = null;
String requestId = theRequest != null ? theRequest.getRequestId() : null;
if (theResource != null) {
if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
IBaseMetaType meta = theResource.getMeta();
source = MetaUtil.getSource(myContext, meta);
}
if (myContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
source = ((IBaseHasExtensions) theResource.getMeta())
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXT_META_SOURCE.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()).getValueAsString())
.findFirst()
.orElse(null);
}
}
boolean haveSource = isNotBlank(source) && myConfig.getStoreMetaSourceInformation().isStoreSourceUri();
boolean haveRequestId = isNotBlank(requestId) && myConfig.getStoreMetaSourceInformation().isStoreRequestId();
if (haveSource || haveRequestId) {
ResourceHistoryProvenanceEntity provenance = new ResourceHistoryProvenanceEntity();
provenance.setResourceHistoryTable(historyEntry);
provenance.setResourceTable(theEntity);
provenance.setPartitionId(theEntity.getPartitionId());
if (haveRequestId) {
provenance.setRequestId(left(requestId, Constants.REQUEST_ID_LENGTH));
}
if (haveSource) {
provenance.setSourceUri(source);
}
myEntityManager.persist(provenance);
}
}
private void validateIncomingResourceTypeMatchesExisting(IBaseResource theResource, ResourceTable entity) { private void validateIncomingResourceTypeMatchesExisting(IBaseResource theResource, ResourceTable entity) {
String resourceType = myContext.getResourceType(theResource); String resourceType = myContext.getResourceType(theResource);
if (!resourceType.equals(entity.getResourceType())) { if (!resourceType.equals(entity.getResourceType())) {

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

@ -51,7 +51,6 @@ import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.patch.FhirPatch; import ca.uhn.fhir.jpa.patch.FhirPatch;
import ca.uhn.fhir.jpa.patch.JsonPatchUtils; import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
import ca.uhn.fhir.jpa.patch.XmlPatchUtils; import ca.uhn.fhir.jpa.patch.XmlPatchUtils;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider; import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum; import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@ -1407,7 +1406,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
} }
} }
translateSearchParams(theParams); translateListSearchParams(theParams);
notifySearchInterceptors(theParams, theRequest); notifySearchInterceptors(theParams, theRequest);
@ -1432,7 +1431,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal; return retVal;
} }
private void translateSearchParams(SearchParameterMap theParams) { private void translateListSearchParams(SearchParameterMap theParams) {
Iterator<String> keyIterator = theParams.keySet().iterator(); Iterator<String> keyIterator = theParams.keySet().iterator();
// Translate _list=42 to _has=List:item:_id=42 // Translate _list=42 to _has=List:item:_id=42