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hapi-fhir
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Merge branch 'master' into custom-elastic-index

This commit is contained in:
Tadgh 2021-09-07 13:56:56 -04:00
parent eabe3e7c74 3e5c2f8bf1
commit 6a2a5d5097
3 changed files with 95 additions and 93 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processor/PidToIBaseResourceProcessor.java
View File

@ -69,7 +69,7 @@ public class PidToIBaseResourceProcessor implements ItemProcessor<List<ResourceP
List<IBaseResource> outgoing = new ArrayList<>(); List<IBaseResource> outgoing = new ArrayList<>();
sb.loadResourcesByPid(theResourcePersistentId, Collections.emptyList(), outgoing, false, null); sb.loadResourcesByPid(theResourcePersistentId, Collections.emptyList(), outgoing, false, null);
ourLog.trace("Loaded resources: {}", outgoing.stream().map(t->t.getIdElement().getValue()).collect(Collectors.joining(", "))); ourLog.trace("Loaded resources: {}", outgoing.stream().filter(t -> t != null).map(t -> t.getIdElement().getValue()).collect(Collectors.joining(", ")));
return outgoing; return outgoing;

181
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -618,49 +618,7 @@ 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) {
Set<ResourceTag> allDefs = new HashSet<>(); changed |= updateTags(theTransactionDetails, theRequest, theResource, theEntity);
Set<ResourceTag> allTagsOld = getAllTagDefinitions(theEntity);
if (theResource instanceof IResource) {
extractTagsHapi(theTransactionDetails, (IResource) theResource, theEntity, allDefs);
} else {
extractTagsRi(theTransactionDetails, (IAnyResource) theResource, theEntity, allDefs);
}
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
if (def.isStandardType() == false) {
String profile = def.getResourceProfile("");
if (isNotBlank(profile)) {
TagDefinition profileDef = getTagOrNull(theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
ResourceTag tag = theEntity.addTag(profileDef);
allDefs.add(tag);
theEntity.setHasTags(true);
}
}
Set<ResourceTag> allTagsNew = getAllTagDefinitions(theEntity);
Set<TagDefinition> allDefsPresent = new HashSet<>();
allTagsNew.forEach(tag -> {
// Don't keep duplicate tags
if (!allDefsPresent.add(tag.getTag())) {
theEntity.getTags().remove(tag);
}
// Drop any tags that have been removed
if (!allDefs.contains(tag)) {
if (shouldDroppedTagBeRemovedOnUpdate(theRequest, tag)) {
theEntity.getTags().remove(tag);
}
}
});
if (!allTagsOld.equals(allTagsNew)) {
changed = true;
}
theEntity.setHasTags(!allTagsNew.isEmpty());
} }
} else { } else {
@ -669,7 +627,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
encoding = ResourceEncodingEnum.DEL; encoding = ResourceEncodingEnum.DEL;
} }
if (thePerformIndexing && changed == false) { if (thePerformIndexing && !changed) {
if (theEntity.getId() == null) { if (theEntity.getId() == null) {
changed = true; changed = true;
} else if (myConfig.isMassIngestionMode()) { } else if (myConfig.isMassIngestionMode()) {
@ -701,6 +659,50 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
return retVal; return retVal;
} }
private boolean updateTags(TransactionDetails theTransactionDetails, RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity) {
Set<ResourceTag> allDefs = new HashSet<>();
Set<ResourceTag> allTagsOld = getAllTagDefinitions(theEntity);
if (theResource instanceof IResource) {
extractTagsHapi(theTransactionDetails, (IResource) theResource, theEntity, allDefs);
} else {
extractTagsRi(theTransactionDetails, (IAnyResource) theResource, theEntity, allDefs);
}
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
if (def.isStandardType() == false) {
String profile = def.getResourceProfile("");
if (isNotBlank(profile)) {
TagDefinition profileDef = getTagOrNull(theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
ResourceTag tag = theEntity.addTag(profileDef);
allDefs.add(tag);
theEntity.setHasTags(true);
}
}
Set<ResourceTag> allTagsNew = getAllTagDefinitions(theEntity);
Set<TagDefinition> allDefsPresent = new HashSet<>();
allTagsNew.forEach(tag -> {
// Don't keep duplicate tags
if (!allDefsPresent.add(tag.getTag())) {
theEntity.getTags().remove(tag);
}
// Drop any tags that have been removed
if (!allDefs.contains(tag)) {
if (shouldDroppedTagBeRemovedOnUpdate(theRequest, tag)) {
theEntity.getTags().remove(tag);
}
}
});
theEntity.setHasTags(!allTagsNew.isEmpty());
return !allTagsOld.equals(allTagsNew);
}
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res, Long theVersion) { private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, @Nullable Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res, Long theVersion) {
R retVal = (R) res; R retVal = (R) res;
@ -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