Add replace-references operation (#6526)
* Rehoming operation * Rename operation * Recover state before moving function to smile Batch job artifacts are very preliminary * Rename rehome to replace_references * Rename rehome to replace_references * spotless * Add message code * Fix op name * Implement plain provider * Add msg code * Fix parameter types fhir version compatibility * spotless * Deduplicate code * Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaSystemProvider.java Implement suggestion Co-authored-by: Ken Stevens <khstevens@gmail.com> * Implement review request: move constant * Change operation interface to use parameters for both source and target reference ids * spotless * Add revision requested todo * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com>
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jmarchionatto
GitHub
parent
9d584d1b83
commit
9bfdbea1ef
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@ -97,8 +97,10 @@ import ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl;
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import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
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import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
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import ca.uhn.fhir.jpa.provider.DiffProvider;
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import ca.uhn.fhir.jpa.provider.IReplaceReferencesSvc;
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import ca.uhn.fhir.jpa.provider.InstanceReindexProvider;
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import ca.uhn.fhir.jpa.provider.ProcessMessageProvider;
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import ca.uhn.fhir.jpa.provider.ReplaceReferencesSvcImpl;
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import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
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import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
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import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
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@ -926,4 +928,9 @@ public class JpaConfig {
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ITagDefinitionDao tagDefinitionDao, MemoryCacheService memoryCacheService) {
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return new CacheTagDefinitionDao(tagDefinitionDao, memoryCacheService);
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}
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@Bean
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public IReplaceReferencesSvc replaceReferencesSvc(FhirContext theFhirContext, DaoRegistry theDaoRegistry) {
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return new ReplaceReferencesSvcImpl(theFhirContext, theDaoRegistry);
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}
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}
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@ -69,6 +69,9 @@ public abstract class BaseJpaSystemProvider<T, MT> extends BaseStorageSystemProv
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@Autowired
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private ITermReadSvc myTermReadSvc;
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@Autowired
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private IReplaceReferencesSvc myReplaceReferencesSvc;
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public BaseJpaSystemProvider() {
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// nothing
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}
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@ -77,6 +80,10 @@ public abstract class BaseJpaSystemProvider<T, MT> extends BaseStorageSystemProv
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return myResourceReindexingSvc;
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}
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public IReplaceReferencesSvc getReplaceReferencesSvc() {
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return myReplaceReferencesSvc;
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}
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@History
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public IBundleProvider historyServer(
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HttpServletRequest theRequest,
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@ -0,0 +1,12 @@
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package ca.uhn.fhir.jpa.provider;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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/**
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* Contract for service which replaces references
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*/
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public interface IReplaceReferencesSvc {
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IBaseParameters replaceReferences(String theSourceRefId, String theTargetRefId, RequestDetails theRequest);
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}
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@ -141,4 +141,17 @@ public final class JpaSystemProvider<T, MT> extends BaseJpaSystemProvider<T, MT>
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endRequest(((ServletRequestDetails) theRequestDetails).getServletRequest());
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}
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}
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@Operation(name = ProviderConstants.OPERATION_REPLACE_REFERENCES, global = true)
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@Description(
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value =
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"This operation searches for all references matching the provided id and updates them to references to the provided newReferenceTargetId.",
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shortDefinition = "Repoints referencing resources to another resources instance")
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public IBaseParameters replaceReferences(
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@OperationParam(name = ProviderConstants.PARAM_SOURCE_REFERENCE_ID) String theSourceId,
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@OperationParam(name = ProviderConstants.PARAM_TARGET_REFERENCE_ID) String theTargetId,
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RequestDetails theRequest) {
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return getReplaceReferencesSvc().replaceReferences(theSourceId, theTargetId, theRequest);
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}
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}
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@ -0,0 +1,221 @@
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package ca.uhn.fhir.jpa.provider;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.model.api.Include;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.PatchTypeEnum;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.util.ResourceReferenceInfo;
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import jakarta.annotation.Nonnull;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeType;
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import org.hl7.fhir.r4.model.Parameters;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.Resource;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.Type;
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import java.security.InvalidParameterException;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import static ca.uhn.fhir.jpa.patch.FhirPatch.OPERATION_REPLACE;
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import static ca.uhn.fhir.jpa.patch.FhirPatch.PARAMETER_OPERATION;
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import static ca.uhn.fhir.jpa.patch.FhirPatch.PARAMETER_PATH;
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import static ca.uhn.fhir.jpa.patch.FhirPatch.PARAMETER_TYPE;
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import static ca.uhn.fhir.jpa.patch.FhirPatch.PARAMETER_VALUE;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_ID;
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import static ca.uhn.fhir.rest.server.provider.ProviderConstants.PARAM_SOURCE_REFERENCE_ID;
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import static ca.uhn.fhir.rest.server.provider.ProviderConstants.PARAM_TARGET_REFERENCE_ID;
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import static software.amazon.awssdk.utils.StringUtils.isBlank;
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public class ReplaceReferencesSvcImpl implements IReplaceReferencesSvc {
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private final FhirContext myFhirContext;
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private final DaoRegistry myDaoRegistry;
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public ReplaceReferencesSvcImpl(FhirContext theFhirContext, DaoRegistry theDaoRegistry) {
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myFhirContext = theFhirContext;
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myDaoRegistry = theDaoRegistry;
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}
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@Override
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public IBaseParameters replaceReferences(String theSourceRefId, String theTargetRefId, RequestDetails theRequest) {
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validateParameters(theSourceRefId, theTargetRefId);
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IIdType sourceRefId = new IdDt(theSourceRefId);
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IIdType targetRefId = new IdDt(theTargetRefId);
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// todo jm: this could be problematic depending on referenceing object set size, however we are adding
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// batch job option to handle that case as part of this feature
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List<? extends IBaseResource> referencingResources = findReferencingResourceIds(sourceRefId, theRequest);
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return replaceReferencesInTransaction(referencingResources, sourceRefId, targetRefId, theRequest);
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}
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private IBaseParameters replaceReferencesInTransaction(
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List<? extends IBaseResource> theReferencingResources,
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IIdType theCurrentTargetId,
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IIdType theNewTargetId,
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RequestDetails theRequest) {
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Parameters resultParams = new Parameters();
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// map resourceType -> map resourceId -> patch Parameters
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Map<String, Map<IIdType, Parameters>> parametersMap =
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buildPatchParameterMap(theReferencingResources, theCurrentTargetId, theNewTargetId);
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for (Map.Entry<String, Map<IIdType, Parameters>> mapEntry : parametersMap.entrySet()) {
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String resourceType = mapEntry.getKey();
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IFhirResourceDao<?> resDao = myDaoRegistry.getResourceDao(resourceType);
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if (resDao == null) {
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throw new InternalErrorException(
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Msg.code(2588) + "No DAO registered for resource type: " + resourceType);
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}
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// patch each resource of resourceType
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patchResourceTypeResources(mapEntry, resDao, resultParams, theRequest);
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}
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return resultParams;
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}
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private void patchResourceTypeResources(
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Map.Entry<String, Map<IIdType, Parameters>> mapEntry,
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IFhirResourceDao<?> resDao,
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Parameters resultParams,
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RequestDetails theRequest) {
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for (Map.Entry<IIdType, Parameters> idParamMapEntry :
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mapEntry.getValue().entrySet()) {
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IIdType resourceId = idParamMapEntry.getKey();
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Parameters parameters = idParamMapEntry.getValue();
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MethodOutcome result =
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resDao.patch(resourceId, null, PatchTypeEnum.FHIR_PATCH_JSON, null, parameters, theRequest);
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resultParams.addParameter().setResource((Resource) result.getOperationOutcome());
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}
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}
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private Map<String, Map<IIdType, Parameters>> buildPatchParameterMap(
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List<? extends IBaseResource> theReferencingResources,
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IIdType theCurrentReferencedResourceId,
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IIdType theNewReferencedResourceId) {
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Map<String, Map<IIdType, Parameters>> paramsMap = new HashMap<>();
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for (IBaseResource referencingResource : theReferencingResources) {
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// resource can have more than one reference to the same target resource
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for (ResourceReferenceInfo refInfo :
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myFhirContext.newTerser().getAllResourceReferences(referencingResource)) {
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addReferenceToMapIfForSource(
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theCurrentReferencedResourceId,
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theNewReferencedResourceId,
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referencingResource,
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refInfo,
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paramsMap);
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}
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}
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return paramsMap;
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}
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private void addReferenceToMapIfForSource(
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IIdType theCurrentReferencedResourceId,
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IIdType theNewReferencedResourceId,
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IBaseResource referencingResource,
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ResourceReferenceInfo refInfo,
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Map<String, Map<IIdType, Parameters>> paramsMap) {
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if (!refInfo.getResourceReference()
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.getReferenceElement()
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.toUnqualifiedVersionless()
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.getValueAsString()
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.equals(theCurrentReferencedResourceId
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.toUnqualifiedVersionless()
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.getValueAsString())) {
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// not a reference to the resource being replaced
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return;
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}
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Parameters.ParametersParameterComponent paramComponent = createReplaceReferencePatchOperation(
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referencingResource.fhirType() + "." + refInfo.getName(),
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new Reference(
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theNewReferencedResourceId.toUnqualifiedVersionless().getValueAsString()));
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paramsMap
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// preserve order, in case it could matter
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.computeIfAbsent(referencingResource.fhirType(), k -> new LinkedHashMap<>())
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.computeIfAbsent(referencingResource.getIdElement(), k -> new Parameters())
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.addParameter(paramComponent);
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}
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@Nonnull
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private Parameters.ParametersParameterComponent createReplaceReferencePatchOperation(
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String thePath, Type theValue) {
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Parameters.ParametersParameterComponent operation = new Parameters.ParametersParameterComponent();
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operation.setName(PARAMETER_OPERATION);
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operation.addPart().setName(PARAMETER_TYPE).setValue(new CodeType(OPERATION_REPLACE));
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operation.addPart().setName(PARAMETER_PATH).setValue(new StringType(thePath));
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operation.addPart().setName(PARAMETER_VALUE).setValue(theValue);
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return operation;
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}
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private List<? extends IBaseResource> findReferencingResourceIds(
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IIdType theSourceRefIdParam, RequestDetails theRequest) {
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IFhirResourceDao<?> dao = getDao(theSourceRefIdParam.getResourceType());
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if (dao == null) {
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throw new InternalErrorException(
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Msg.code(2582) + "Couldn't obtain DAO for resource type" + theSourceRefIdParam.getResourceType());
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}
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SearchParameterMap parameterMap = new SearchParameterMap();
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parameterMap.add(PARAM_ID, new StringParam(theSourceRefIdParam.getValue()));
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parameterMap.addRevInclude(new Include("*"));
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return dao.search(parameterMap, theRequest).getAllResources();
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}
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private IFhirResourceDao<?> getDao(String theResourceName) {
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return myDaoRegistry.getResourceDao(theResourceName);
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}
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private void validateParameters(String theSourceRefIdParam, String theTargetRefIdParam) {
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if (isBlank(theSourceRefIdParam)) {
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throw new InvalidParameterException(
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Msg.code(2583) + "Parameter '" + PARAM_SOURCE_REFERENCE_ID + "' is blank");
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}
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if (isBlank(theTargetRefIdParam)) {
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throw new InvalidParameterException(
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Msg.code(2584) + "Parameter '" + PARAM_TARGET_REFERENCE_ID + "' is blank");
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}
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IIdType sourceId = new IdDt(theSourceRefIdParam);
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if (isBlank(sourceId.getResourceType())) {
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throw new InvalidParameterException(
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Msg.code(2585) + "'" + PARAM_SOURCE_REFERENCE_ID + "' must be a resource type qualified id");
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}
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IIdType targetId = new IdDt(theTargetRefIdParam);
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if (isBlank(targetId.getResourceType())) {
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throw new InvalidParameterException(
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Msg.code(2586) + "'" + PARAM_TARGET_REFERENCE_ID + "' must be a resource type qualified id");
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}
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if (!targetId.getResourceType().equals(sourceId.getResourceType())) {
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throw new InvalidParameterException(
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Msg.code(2587) + "Source and target id parameters must be for the same resource type");
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}
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}
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}
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@ -239,8 +239,24 @@ public class ProviderConstants {
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* Operation name for the "$export-poll-status" operation
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*/
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public static final String OPERATION_EXPORT_POLL_STATUS = "$export-poll-status";
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/**
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* Operation name for the "$export" operation
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*/
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public static final String OPERATION_EXPORT = "$export";
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/**
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* Operation name for the "$replace-references" operation
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*/
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public static final String OPERATION_REPLACE_REFERENCES = "$replace-references";
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/**
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* Parameter for source reference of the "$replace-references" operation
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*/
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public static final String PARAM_SOURCE_REFERENCE_ID = "sourceReferenceId";
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/**
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* Parameter for target reference of the "$replace-references" operation
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*/
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public static final String PARAM_TARGET_REFERENCE_ID = "targetReferenceId";
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}
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