Add MDM expansion by golden pid
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@ -75,6 +75,7 @@ public enum VersionEnum {
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V5_4_1,
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V5_4_2,
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V5_5_0,
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;
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public static VersionEnum latestVersion() {
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@ -0,0 +1,5 @@
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---
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type: add
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issue: 2871
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title: "Modified the behaviour of the `:mdm` param qualifier. Previously, it used to only resolve IDs if the resource ID was a source resource.
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Now, MDM expansion will work if you pass it the ID of a golden resource instead."
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@ -67,4 +67,7 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
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"AND ml.myMatchResult=:matchResult")
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List<MdmPidTuple> expandPidsBySourcePidAndMatchResult(@Param("sourcePid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
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@Query("SELECT ml.myGoldenResourcePid as goldenPid, ml.mySourcePid as sourcePid FROM MdmLink ml WHERE ml.myGoldenResourcePid = :goldenPid and ml.myMatchResult = :matchResult")
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List<MdmPidTuple> expandPidsByGoldenResourcePidAndMatchResult(@Param("goldenPid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
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}
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@ -25,15 +25,13 @@ import ca.uhn.fhir.jpa.dao.index.IdHelperService;
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import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
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import ca.uhn.fhir.mdm.log.Logs;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import java.util.ArrayList;
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import javax.annotation.Nonnull;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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@ -82,14 +80,50 @@ public class MdmLinkExpandSvc {
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public Set<String> expandMdmBySourceResourcePid(Long theSourceResourcePid) {
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ourLog.debug("About to expand source resource with PID {}", theSourceResourcePid);
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List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
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return flattenPidTuplesToSet(theSourceResourcePid, goldenPidSourcePidTuples);
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}
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/**
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* Given a PID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
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* MDM-Matched to this golden resource.
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*
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* @param theGoldenResourcePid The PID of the golden resource to MDM-Expand.
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* @return A set of strings representing the FHIR ids of the expanded resources.
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*/
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public Set<String> expandMdmByGoldenResourceId(Long theGoldenResourcePid) {
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ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
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List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
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return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
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}
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/**
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* Given a resource ID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
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* MDM-Matched to this golden resource.
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*
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* @param theGoldenResourcePid The resource ID of the golden resource to MDM-Expand.
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* @return A set of strings representing the FHIR ids of the expanded resources.
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*/
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public Set<String> expandMdmByGoldenResourcePid(Long theGoldenResourcePid) {
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ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
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List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
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return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
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}
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public Set<String> expandMdmByGoldenResourceId(IdDt theId) {
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ourLog.debug("About to expand golden resource with golden resource id {}", theId);
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Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
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return expandMdmByGoldenResourcePid(pidOrThrowException);
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}
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@Nonnull
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private Set<String> flattenPidTuplesToSet(Long initialPid, List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples) {
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Set<Long> flattenedPids = new HashSet<>();
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goldenPidSourcePidTuples.forEach(tuple -> {
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flattenedPids.add(tuple.getSourcePid());
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flattenedPids.add(tuple.getGoldenPid());
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});
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Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
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ourLog.debug("Pid {} has been expanded to [{}]", theSourceResourcePid, String.join(",", resourceIds));
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ourLog.debug("Pid {} has been expanded to [{}]", initialPid, String.join(",", resourceIds));
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return resourceIds;
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}
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}
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@ -76,8 +76,16 @@ public class MdmSearchExpandingInterceptor {
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if (iQueryParameterType instanceof ReferenceParam) {
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ReferenceParam refParam = (ReferenceParam) iQueryParameterType;
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if (refParam.isMdmExpand()) {
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ourLog.debug("Found a reference parameter to expand: {}", refParam.toString());
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ourLog.debug("Found a reference parameter to expand: {}", refParam);
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//First, attempt to expand as a source resource.
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Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(refParam.getValue()));
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// If we failed, attempt to expand as a golden resource
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if (expandedResourceIds.isEmpty()) {
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expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
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}
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//Rebuild the search param list.
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if (!expandedResourceIds.isEmpty()) {
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ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
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toRemove.add(refParam);
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@ -2,14 +2,18 @@ package ca.uhn.fhir.jpa.mdm.interceptor;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
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import ca.uhn.fhir.jpa.entity.MdmLink;
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import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
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import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
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import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.mdm.api.MdmConstants;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.rest.param.ReferenceOrListParam;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import org.elasticsearch.common.collect.Set;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Patient;
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@ -21,6 +25,8 @@ import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.annotation.DirtiesContext;
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import org.springframework.test.context.ContextConfiguration;
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import java.util.List;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.equalTo;
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import static org.hamcrest.Matchers.is;
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@ -73,6 +79,19 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
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myDaoConfig.setAllowMdmExpansion(true);
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search = myObservationDao.search(searchParameterMap);
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assertThat(search.size(), is(equalTo(4)));
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List<MdmLink> all = myMdmLinkDao.findAll();
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Long goldenPid = all.get(0).getGoldenResourcePid();
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IIdType goldenId = myIdHelperService.translatePidIdToForcedId(myFhirContext, "Patient", new ResourcePersistentId(goldenPid));
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//Verify that expansion by the golden resource id resolves down to everything its links have.
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SearchParameterMap goldenSpMap = new SearchParameterMap();
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goldenSpMap.setLoadSynchronous(true);
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ReferenceOrListParam goldenReferenceOrListParam = new ReferenceOrListParam();
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goldenReferenceOrListParam.addOr(new ReferenceParam(goldenId).setMdmExpand(true));
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goldenSpMap.add(Observation.SP_SUBJECT, goldenReferenceOrListParam);
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search = myObservationDao.search(goldenSpMap);
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assertThat(search.size(), is(equalTo(4)));
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}
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@Test
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