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create merge provenance resource #6596

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create merge provenance resource #6596

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2d92405
create merge provenance resource
mrdnctrk Jan 3, 2025
27fb693
merge master
Jan 8, 2025
fbdc484
Merge branch 'master' into emre-merge-provenance
mrdnctrk Jan 10, 2025
6c1331e
added provenance to replace-references and added provenance tests for…
mrdnctrk Jan 9, 2025
b699e44
minor code cleanup
mrdnctrk Jan 10, 2025
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaSystemProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,7 @@ public IBaseParameters replaceReferences(
RequestPartitionId partitionId = myRequestPartitionHelperSvc.determineReadPartitionForRequest(
theServletRequest, ReadPartitionIdRequestDetails.forRead(targetId));
ReplaceReferencesRequest replaceReferencesRequest =
new ReplaceReferencesRequest(sourceId, targetId, resourceLimit, partitionId);
new ReplaceReferencesRequest(sourceId, targetId, resourceLimit, partitionId, true);
IBaseParameters retval =
getReplaceReferencesSvc().replaceReferences(replaceReferencesRequest, theServletRequest);
if (ParametersUtil.getNamedParameter(getContext(), retval, OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_TASK)
Expand Down
15 changes: 15 additions & 0 deletions ...-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/ReplaceReferencesSvcImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@

import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.jobs.replacereferences.ReplaceReferencesJobParameters;
import ca.uhn.fhir.batch2.jobs.replacereferences.ReplaceReferencesProvenanceSvc;
import ca.uhn.fhir.batch2.util.Batch2TaskHelper;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
Expand All @@ -42,6 +43,8 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.Date;
import java.util.List;
import java.util.stream.Stream;

import static ca.uhn.fhir.batch2.jobs.replacereferences.ReplaceReferencesAppCtx.JOB_REPLACE_REFERENCES;
Expand All @@ -58,6 +61,7 @@ public class ReplaceReferencesSvcImpl implements IReplaceReferencesSvc {
private final ReplaceReferencesPatchBundleSvc myReplaceReferencesPatchBundleSvc;
private final Batch2TaskHelper myBatch2TaskHelper;
private final JpaStorageSettings myStorageSettings;
private final ReplaceReferencesProvenanceSvc myReplaceReferencesProvenanceSvc;

public ReplaceReferencesSvcImpl(
DaoRegistry theDaoRegistry,
Expand All @@ -74,6 +78,7 @@ public ReplaceReferencesSvcImpl(
myReplaceReferencesPatchBundleSvc = theReplaceReferencesPatchBundleSvc;
myBatch2TaskHelper = theBatch2TaskHelper;
myStorageSettings = theStorageSettings;
myReplaceReferencesProvenanceSvc = new ReplaceReferencesProvenanceSvc(theDaoRegistry);
}

@Override
Expand Down Expand Up @@ -123,6 +128,7 @@ private IBaseParameters replaceReferencesPreferAsync(
private IBaseParameters replaceReferencesPreferSync(
ReplaceReferencesRequest theReplaceReferencesRequest, RequestDetails theRequestDetails) {

Date startTime = new Date();
// TODO KHS get partition from request
StopLimitAccumulator<IdDt> accumulator = myHapiTransactionService
.withRequest(theRequestDetails)
Expand All @@ -139,6 +145,15 @@ private IBaseParameters replaceReferencesPreferSync(
Bundle result = myReplaceReferencesPatchBundleSvc.patchReferencingResources(
theReplaceReferencesRequest, accumulator.getItemList(), theRequestDetails);

if (theReplaceReferencesRequest.createProvenance) {
myReplaceReferencesProvenanceSvc.createProvenance(
theReplaceReferencesRequest.targetId,
theReplaceReferencesRequest.sourceId,
List.of(result),
startTime,
theRequestDetails);
}

Parameters retval = new Parameters();
retval.addParameter()
.setName(OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_OUTCOME)
Expand Down
40 changes: 33 additions & 7 deletions ...hir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/merge/ResourceMergeService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@

import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.jobs.merge.MergeJobParameters;
import ca.uhn.fhir.batch2.jobs.merge.MergeProvenanceSvc;
import ca.uhn.fhir.batch2.jobs.merge.MergeResourceHelper;
import ca.uhn.fhir.batch2.util.Batch2TaskHelper;
import ca.uhn.fhir.context.FhirContext;
Expand All @@ -36,17 +37,24 @@
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Task;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.Date;
import java.util.List;

import static ca.uhn.fhir.batch2.jobs.merge.MergeAppCtx.JOB_MERGE;
import static ca.uhn.fhir.rest.api.Constants.STATUS_HTTP_200_OK;
import static ca.uhn.fhir.rest.api.Constants.STATUS_HTTP_202_ACCEPTED;
import static ca.uhn.fhir.rest.api.Constants.STATUS_HTTP_500_INTERNAL_ERROR;
import static ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_OUTCOME;

/**
* Service for the FHIR $merge operation. Currently only supports Patient/$merge. The plan is to expand to other resource types.
Expand All @@ -65,6 +73,7 @@ public class ResourceMergeService {
private final MergeResourceHelper myMergeResourceHelper;
private final Batch2TaskHelper myBatch2TaskHelper;
private final MergeValidationService myMergeValidationService;
private final MergeProvenanceSvc myMergeProvenanceSvc;

public ResourceMergeService(
JpaStorageSettings theStorageSettings,
Expand All @@ -84,13 +93,18 @@ public ResourceMergeService(
myBatch2TaskHelper = theBatch2TaskHelper;
myFhirContext = myPatientDao.getContext();
myHapiTransactionService = theHapiTransactionService;
myMergeResourceHelper = new MergeResourceHelper(myPatientDao);
myMergeProvenanceSvc = new MergeProvenanceSvc(theDaoRegistry);
myMergeResourceHelper = new MergeResourceHelper(theDaoRegistry, myMergeProvenanceSvc);
myMergeValidationService = new MergeValidationService(myFhirContext, theDaoRegistry);
}

/**
* Perform the $merge operation. If the number of resources to be changed exceeds the provided batch size,
* then switch to async mode. See the <a href="https://build.fhir.org/patient-operation-merge.html">Patient $merge spec</a>
* Perform the $merge operation. Operation can be performed synchronously or asynchronously depending on
* the prefer-async request header.
* If the operation is requested to be performed synchronously and the number of
* resources to be changed exceeds the provided batch size,
* and error is returned indicating that operation needs to be performed asynchronously. See the
* <a href="https://build.fhir.org/patient-operation-merge.html">Patient $merge spec</a>
* for details on what the difference is between synchronous and asynchronous mode.
*
* @param theMergeOperationParameters the merge operation parameters
Expand Down Expand Up @@ -211,21 +225,33 @@ private void doMergeSync(
MergeOperationOutcome theMergeOutcome,
RequestPartitionId partitionId) {

Date startTime = new Date();
ReplaceReferencesRequest replaceReferencesRequest = new ReplaceReferencesRequest(
theSourceResource.getIdElement(),
theTargetResource.getIdElement(),
theMergeOperationParameters.getResourceLimit(),
partitionId);
partitionId,
// don't create provenance as part of replace-references,
// we create it after updating source and target for merge
false);

IBaseParameters outParams =
myReplaceReferencesSvc.replaceReferences(replaceReferencesRequest, theRequestDetails);

myReplaceReferencesSvc.replaceReferences(replaceReferencesRequest, theRequestDetails);
Bundle patchResultBundle = (Bundle) ParametersUtil.getNamedParameterResource(
myFhirContext, outParams, OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_OUTCOME)
.orElseThrow();

Patient updatedTarget = myMergeResourceHelper.updateMergedResourcesAfterReferencesReplaced(
Patient updatedTarget = myMergeResourceHelper.updateMergedResourcesAndCreateProvenance(
myHapiTransactionService,
theSourceResource,
theTargetResource,
List.of(patchResultBundle),
(Patient) theMergeOperationParameters.getResultResource(),
theMergeOperationParameters.getDeleteSource(),
theRequestDetails);
theRequestDetails,
startTime);

theMergeOutcome.setUpdatedTargetResource(updatedTarget);

String detailsText = "Merge operation completed successfully.";
Expand Down
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