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hapi-fhir
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Use dynamic projection

This commit is contained in:
Tadgh 2021-03-29 11:38:52 -04:00
parent 002d3fcf3c
commit c46617fefa
3 changed files with 26 additions and 15 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/GoldenResourceAnnotatingProcessor.java
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@ -117,8 +117,6 @@ public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBa
IBaseExtension<?, ?> extension = ExtensionUtil.getOrCreateExtension(iBaseResource, HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL); IBaseExtension<?, ?> extension = ExtensionUtil.getOrCreateExtension(iBaseResource, HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL);
if (!StringUtils.isBlank(goldenResourceId)) { if (!StringUtils.isBlank(goldenResourceId)) {
ExtensionUtil.setExtension(myContext, extension, "reference", prefixPatient(goldenResourceId)); ExtensionUtil.setExtension(myContext, extension, "reference", prefixPatient(goldenResourceId));
} else {
ExtensionUtil.setExtension(myContext, extension, "string", "This patient has no matched golden resource.");
} }
} }

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java
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@ -120,8 +120,11 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
if (myMdmEnabled) { if (myMdmEnabled) {
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId)); IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
Long pidOrNull = myIdHelperService.getPidOrNull(group); Long pidOrNull = myIdHelperService.getPidOrNull(group);
List<List<Long>> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH); List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
goldenPidSourcePidTuple.forEach(patientPidsToExport::addAll); goldenPidSourcePidTuple.forEach(tuple -> {
patientPidsToExport.add(tuple.getGoldenPid());
patientPidsToExport.add(tuple.getSourcePid());
});
populateMdmResourceCache(goldenPidSourcePidTuple); populateMdmResourceCache(goldenPidSourcePidTuple);
} }
List<ResourcePersistentId> resourcePersistentIds = patientPidsToExport List<ResourcePersistentId> resourcePersistentIds = patientPidsToExport
@ -134,7 +137,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
/** /**
* @param thePidTuples * @param thePidTuples
*/ */
private void populateMdmResourceCache(List<List<Long>> thePidTuples) { private void populateMdmResourceCache(List<IMdmLinkDao.MdmPidTuple> thePidTuples) {
if (myMdmExpansionCacheSvc.hasBeenPopulated()) { if (myMdmExpansionCacheSvc.hasBeenPopulated()) {
return; return;
} }
@ -144,9 +147,9 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
// patient/gold-2 -> [patient/3, patient/4] // patient/gold-2 -> [patient/3, patient/4]
//} //}
Map<Long, Set<Long>> goldenResourceToSourcePidMap = new HashMap<>(); Map<Long, Set<Long>> goldenResourceToSourcePidMap = new HashMap<>();
for (List<Long> goldenPidTargetPidTuple : thePidTuples) { for (IMdmLinkDao.MdmPidTuple goldenPidTargetPidTuple : thePidTuples) {
Long goldenPid = goldenPidTargetPidTuple.get(0); Long goldenPid = goldenPidTargetPidTuple.getGoldenPid();
Long sourcePid = goldenPidTargetPidTuple.get(1); Long sourcePid = goldenPidTargetPidTuple.getSourcePid();
if(!goldenResourceToSourcePidMap.containsKey(goldenPid)) { if(!goldenResourceToSourcePidMap.containsKey(goldenPid)) {
goldenResourceToSourcePidMap.put(goldenPid, new HashSet<>()); goldenResourceToSourcePidMap.put(goldenPid, new HashSet<>());
@ -204,16 +207,19 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
//Attempt to perform MDM Expansion of membership //Attempt to perform MDM Expansion of membership
if (myMdmEnabled) { if (myMdmEnabled) {
List<List<Long>> goldenPidTargetPidTuples = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH); List<IMdmLinkDao.MdmPidTuple> goldenPidTargetPidTuples = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
//Now lets translate these pids into resource IDs //Now lets translate these pids into resource IDs
Set<Long> uniquePids = new HashSet<>(); Set<Long> uniquePids = new HashSet<>();
goldenPidTargetPidTuples.forEach(uniquePids::addAll); goldenPidTargetPidTuples.forEach(tuple -> {
uniquePids.add(tuple.getGoldenPid());
uniquePids.add(tuple.getSourcePid());
});
Map<Long, Optional<String>> pidToForcedIdMap = myIdHelperService.translatePidsToForcedIds(uniquePids); Map<Long, Optional<String>> pidToForcedIdMap = myIdHelperService.translatePidsToForcedIds(uniquePids);
Map<Long, Set<Long>> goldenResourceToSourcePidMap = new HashMap<>(); Map<Long, Set<Long>> goldenResourceToSourcePidMap = new HashMap<>();
for (List<Long> goldenPidTargetPidTuple : goldenPidTargetPidTuples) { for (IMdmLinkDao.MdmPidTuple goldenPidTargetPidTuple : goldenPidTargetPidTuples) {
Long goldenPid = goldenPidTargetPidTuple.get(0); Long goldenPid = goldenPidTargetPidTuple.getGoldenPid();
Long sourcePid = goldenPidTargetPidTuple.get(1); Long sourcePid = goldenPidTargetPidTuple.getSourcePid();
if(!goldenResourceToSourcePidMap.containsKey(goldenPid)) { if(!goldenResourceToSourcePidMap.containsKey(goldenPid)) {
goldenResourceToSourcePidMap.put(goldenPid, new HashSet<>()); goldenResourceToSourcePidMap.put(goldenPid, new HashSet<>());

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IMdmLinkDao.java
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum; import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.jpa.entity.MdmLink; import ca.uhn.fhir.jpa.entity.MdmLink;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.data.jpa.repository.JpaRepository; import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying; import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query; import org.springframework.data.jpa.repository.Query;
@ -40,7 +41,7 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
@Query("DELETE FROM MdmLink f WHERE (myGoldenResourcePid = :pid OR mySourcePid = :pid) AND myMatchResult <> :matchResult") @Query("DELETE FROM MdmLink f WHERE (myGoldenResourcePid = :pid OR mySourcePid = :pid) AND myMatchResult <> :matchResult")
int deleteWithAnyReferenceToPidAndMatchResultNot(@Param("pid") Long thePid, @Param("matchResult") MdmMatchResultEnum theMatchResult); int deleteWithAnyReferenceToPidAndMatchResultNot(@Param("pid") Long thePid, @Param("matchResult") MdmMatchResultEnum theMatchResult);
@Query("SELECT ml2.myGoldenResourcePid, ml2.mySourcePid FROM MdmLink ml2 " + @Query("SELECT ml2.myGoldenResourcePid as goldenPid, ml2.mySourcePid as sourcePid FROM MdmLink ml2 " +
"WHERE ml2.myMatchResult=:matchResult " + "WHERE ml2.myMatchResult=:matchResult " +
"AND ml2.myGoldenResourcePid IN (" + "AND ml2.myGoldenResourcePid IN (" +
"SELECT ml.myGoldenResourcePid FROM MdmLink ml " + "SELECT ml.myGoldenResourcePid FROM MdmLink ml " +
@ -50,5 +51,11 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
"AND hrl.mySourcePath='Group.member.entity' " + "AND hrl.mySourcePath='Group.member.entity' " +
"AND hrl.myTargetResourceType='Patient'" + "AND hrl.myTargetResourceType='Patient'" +
")") ")")
List<List<Long>> expandPidsFromGroupPidGivenMatchResult(@Param("groupPid") Long theGroupPid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum); List<MdmPidTuple> expandPidsFromGroupPidGivenMatchResult(@Param("groupPid") Long theGroupPid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
interface MdmPidTuple {
Long getGoldenPid();
Long getSourcePid();
}
} }