ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc Maven / Gradle / Ivy
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* HAPI FHIR JPA Server - Master Data Management
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* Licensed under the Apache License, Version 2.0 (the "License");
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* http://www.apache.org/licenses/LICENSE-2.0
*
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package ca.uhn.fhir.jpa.mdm.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmLinkWithRevision;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.params.MdmHistorySearchParameters;
import ca.uhn.fhir.mdm.api.params.MdmQuerySearchParameters;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.dao.MdmLinkFactory;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Example;
import org.springframework.data.domain.Page;
import org.springframework.data.history.Revisions;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Optional;
public class MdmLinkDaoSvc> {
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
private IMdmLinkDao myMdmLinkDao;
@Autowired
private MdmLinkFactory myMdmLinkFactory;
@Autowired
private IIdHelperService myIdHelperService;
@Autowired
private FhirContext myFhirContext;
@Transactional
public M createOrUpdateLinkEntity(
IAnyResource theGoldenResource,
IAnyResource theSourceResource,
MdmMatchOutcome theMatchOutcome,
MdmLinkSourceEnum theLinkSource,
@Nullable MdmTransactionContext theMdmTransactionContext) {
M mdmLink = getOrCreateMdmLinkByGoldenResourceAndSourceResource(theGoldenResource, theSourceResource);
mdmLink.setLinkSource(theLinkSource);
mdmLink.setMatchResult(theMatchOutcome.getMatchResultEnum());
// Preserve these flags for link updates
mdmLink.setEidMatch(theMatchOutcome.isEidMatch() | mdmLink.isEidMatchPresent());
mdmLink.setHadToCreateNewGoldenResource(
theMatchOutcome.isCreatedNewResource() | mdmLink.getHadToCreateNewGoldenResource());
mdmLink.setMdmSourceType(myFhirContext.getResourceType(theSourceResource));
setScoreProperties(theMatchOutcome, mdmLink);
// Add partition for the mdm link if it's available in the source resource
RequestPartitionId partitionId =
(RequestPartitionId) theSourceResource.getUserData(Constants.RESOURCE_PARTITION_ID);
if (partitionId != null && partitionId.getFirstPartitionIdOrNull() != null) {
mdmLink.setPartitionId(new PartitionablePartitionId(
partitionId.getFirstPartitionIdOrNull(), partitionId.getPartitionDate()));
}
String message = String.format(
"Creating %s link from %s to Golden Resource %s.",
mdmLink.getMatchResult(),
theSourceResource.getIdElement().toUnqualifiedVersionless(),
theGoldenResource.getIdElement().toUnqualifiedVersionless());
theMdmTransactionContext.addTransactionLogMessage(message);
ourLog.debug(message);
save(mdmLink);
return mdmLink;
}
private void setScoreProperties(MdmMatchOutcome theMatchOutcome, M mdmLink) {
if (theMatchOutcome.getScore() != null) {
mdmLink.setScore(
mdmLink.getScore() != null
? Math.max(theMatchOutcome.getNormalizedScore(), mdmLink.getScore())
: theMatchOutcome.getNormalizedScore());
}
if (theMatchOutcome.getVector() != null) {
mdmLink.setVector(
mdmLink.getVector() != null
? Math.max(theMatchOutcome.getVector(), mdmLink.getVector())
: theMatchOutcome.getVector());
}
mdmLink.setRuleCount(
mdmLink.getRuleCount() != null
? Math.max(theMatchOutcome.getMdmRuleCount(), mdmLink.getRuleCount())
: theMatchOutcome.getMdmRuleCount());
}
@Nonnull
public M getOrCreateMdmLinkByGoldenResourceAndSourceResource(
IAnyResource theGoldenResource, IAnyResource theSourceResource) {
P goldenResourcePid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
P sourceResourcePid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
Optional oExisting = getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourcePid, sourceResourcePid);
if (oExisting.isPresent()) {
return oExisting.get();
} else {
M newLink = myMdmLinkFactory.newMdmLink();
newLink.setGoldenResourcePersistenceId(goldenResourcePid);
newLink.setSourcePersistenceId(sourceResourcePid);
return newLink;
}
}
/**
* Given a golden resource Pid and source Pid, return the mdm link that matches these criterias if exists
*
* @param theGoldenResourcePid
* @param theSourceResourcePid
* @return
* @deprecated This was deprecated in favour of using ResourcePersistenceId rather than longs
*/
@Deprecated
public Optional getLinkByGoldenResourcePidAndSourceResourcePid(
Long theGoldenResourcePid, Long theSourceResourcePid) {
return getLinkByGoldenResourcePidAndSourceResourcePid(
myIdHelperService.newPid(theGoldenResourcePid), myIdHelperService.newPid(theSourceResourcePid));
}
/**
* Given a golden resource Pid and source Pid, return the mdm link that matches these criterias if exists
* @param theGoldenResourcePid The ResourcePersistenceId of the golden resource
* @param theSourceResourcePid The ResourcepersistenceId of the Source resource
* @return The {@link IMdmLink} entity that matches these criteria if exists
*/
public Optional getLinkByGoldenResourcePidAndSourceResourcePid(P theGoldenResourcePid, P theSourceResourcePid) {
if (theSourceResourcePid == null || theGoldenResourcePid == null) {
return Optional.empty();
}
M link = myMdmLinkFactory.newMdmLinkVersionless();
link.setSourcePersistenceId(theSourceResourcePid);
link.setGoldenResourcePersistenceId(theGoldenResourcePid);
// TODO - replace the use of example search
Example example = Example.of(link);
return myMdmLinkDao.findOne(example);
}
/**
* Given a source resource Pid, and a match result, return all links that match these criteria.
*
* @param theSourcePid the source of the relationship.
* @param theMatchResult the Match Result of the relationship
* @return a list of {@link IMdmLink} entities matching these criteria.
*/
public List getMdmLinksBySourcePidAndMatchResult(P theSourcePid, MdmMatchResultEnum theMatchResult) {
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setSourcePersistenceId(theSourcePid);
exampleLink.setMatchResult(theMatchResult);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
/**
* Given a source Pid, return its Matched {@link IMdmLink}. There can only ever be at most one of these, but its possible
* the source has no matches, and may return an empty optional.
*
* @param theSourcePid The Pid of the source you wish to find the matching link for.
* @return the {@link IMdmLink} that contains the Match information for the source.
*/
@Deprecated
@Transactional
public Optional getMatchedLinkForSourcePid(P theSourcePid) {
return myMdmLinkDao.findBySourcePidAndMatchResult(theSourcePid, MdmMatchResultEnum.MATCH);
}
/**
* Given an IBaseResource, return its Matched {@link IMdmLink}. There can only ever be at most one of these, but its possible
* the source has no matches, and may return an empty optional.
*
* @param theSourceResource The IBaseResource representing the source you wish to find the matching link for.
* @return the {@link IMdmLink} that contains the Match information for the source.
*/
public Optional getMatchedLinkForSource(IBaseResource theSourceResource) {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.MATCH);
}
public Optional getPossibleMatchedLinkForSource(IBaseResource theSourceResource) {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.POSSIBLE_MATCH);
}
@Nonnull
private Optional getMdmLinkWithMatchResult(IBaseResource theSourceResource, MdmMatchResultEnum theMatchResult) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
if (pid == null) {
return Optional.empty();
}
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setSourcePersistenceId(pid);
exampleLink.setMatchResult(theMatchResult);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
/**
* Given a golden resource a source and a match result, return the matching {@link IMdmLink}, if it exists.
*
* @param theGoldenResourcePid The Pid of the Golden Resource in the relationship
* @param theSourcePid The Pid of the source in the relationship
* @param theMatchResult The MatchResult you are looking for.
* @return an Optional {@link IMdmLink} containing the matched link if it exists.
*/
public Optional getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(
Long theGoldenResourcePid, Long theSourcePid, MdmMatchResultEnum theMatchResult) {
return getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(
myIdHelperService.newPid(theGoldenResourcePid), myIdHelperService.newPid(theSourcePid), theMatchResult);
}
public Optional getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(
P theGoldenResourcePid, P theSourcePid, MdmMatchResultEnum theMatchResult) {
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setGoldenResourcePersistenceId(theGoldenResourcePid);
exampleLink.setSourcePersistenceId(theSourcePid);
exampleLink.setMatchResult(theMatchResult);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
/**
* Get all {@link IMdmLink} which have {@link MdmMatchResultEnum#POSSIBLE_DUPLICATE} as their match result.
*
* @return A list of {@link IMdmLink} that hold potential duplicate golden resources.
*/
public List getPossibleDuplicates() {
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
@Transactional
public Optional findMdmLinkBySource(IBaseResource theSourceResource) {
@Nullable P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
if (pid == null) {
return Optional.empty();
}
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setSourcePersistenceId(pid);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
/**
* Delete a given {@link IMdmLink}. Note that this does not clear out the Golden resource.
* It is a simple entity delete.
*
* @param theMdmLink the {@link IMdmLink} to delete.
*/
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void deleteLink(M theMdmLink) {
myMdmLinkDao.validateMdmLink(theMdmLink);
myMdmLinkDao.delete(theMdmLink);
}
/**
* Given a Golden Resource, return all links in which they are the source Golden Resource of the {@link IMdmLink}
*
* @param theGoldenResource The {@link IBaseResource} Golden Resource who's links you would like to retrieve.
* @return A list of all {@link IMdmLink} entities in which theGoldenResource is the source Golden Resource
*/
@Transactional
public List findMdmLinksByGoldenResource(IBaseResource theGoldenResource) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
if (pid == null) {
return Collections.emptyList();
}
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setGoldenResourcePersistenceId(pid);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
/**
* Persist an MDM link to the database.
*
* @param theMdmLink the link to save.
* @return the persisted {@link IMdmLink} entity.
*/
public M save(M theMdmLink) {
M mdmLink = myMdmLinkDao.validateMdmLink(theMdmLink);
if (mdmLink.getCreated() == null) {
mdmLink.setCreated(new Date());
}
mdmLink.setUpdated(new Date());
return myMdmLinkDao.save(mdmLink);
}
/**
* Given a list of criteria, return all links from the database which fits the criteria provided
*
* @param theMdmQuerySearchParameters The {@link MdmQuerySearchParameters} being searched.
* @return a list of {@link IMdmLink} entities which match the example.
*/
public Page executeTypedQuery(MdmQuerySearchParameters theMdmQuerySearchParameters) {
return myMdmLinkDao.search(theMdmQuerySearchParameters);
}
/**
* Given a source {@link IBaseResource}, return all {@link IMdmLink} entities in which this source is the source
* of the relationship. This will show you all links for a given Patient/Practitioner.
*
* @param theSourceResource the source resource to find links for.
* @return all links for the source.
*/
@Transactional
public List findMdmLinksBySourceResource(IBaseResource theSourceResource) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
if (pid == null) {
return Collections.emptyList();
}
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setSourcePersistenceId(pid);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
/**
* Finds all {@link IMdmLink} entities in which theGoldenResource's PID is the source
* of the relationship.
*
* @param theGoldenResource the source resource to find links for.
* @return all links for the source.
*/
public List findMdmMatchLinksByGoldenResource(IBaseResource theGoldenResource) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
if (pid == null) {
return Collections.emptyList();
}
M exampleLink = myMdmLinkFactory.newMdmLinkVersionless();
exampleLink.setGoldenResourcePersistenceId(pid);
exampleLink.setMatchResult(MdmMatchResultEnum.MATCH);
Example example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
/**
* Factory delegation method, whenever you need a new MdmLink, use this factory method.
* //TODO Should we make the constructor private for MdmLink? or work out some way to ensure they can only be instantiated via factory.
*
* @return A new {@link IMdmLink}.
*/
public IMdmLink newMdmLink() {
return myMdmLinkFactory.newMdmLink();
}
public Optional getMatchedOrPossibleMatchedLinkForSource(IAnyResource theResource) {
// TODO KHS instead of two queries, just do one query with an OR
Optional retval = getMatchedLinkForSource(theResource);
if (!retval.isPresent()) {
retval = getPossibleMatchedLinkForSource(theResource);
}
return retval;
}
public Optional getLinkByGoldenResourceAndSourceResource(
@Nullable IAnyResource theGoldenResource, @Nullable IAnyResource theSourceResource) {
if (theGoldenResource == null || theSourceResource == null) {
return Optional.empty();
}
return getLinkByGoldenResourcePidAndSourceResourcePid(
myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource),
myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource));
}
@Transactional(propagation = Propagation.MANDATORY)
public void deleteLinksWithAnyReferenceToPids(List theGoldenResourcePids) {
myMdmLinkDao.deleteLinksWithAnyReferenceToPids(theGoldenResourcePids);
}
// TODO: LD: delete for good on the next bump
@Deprecated(since = "6.5.7", forRemoval = true)
public Revisions findMdmLinkHistory(M mdmLink) {
return myMdmLinkDao.findHistory(mdmLink.getId());
}
@Transactional
public List> findMdmLinkHistory(MdmHistorySearchParameters theMdmHistorySearchParameters) {
return myMdmLinkDao.getHistoryForIds(theMdmHistorySearchParameters);
}
}