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MDM virtualization

This commit is contained in:
James Agnew 2024-11-13 15:41:27 -05:00
parent 7c98bfdd9f
commit 0e1be114ee
3 changed files with 93 additions and 28 deletions
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4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmReadVirtualizationInterceptorTest.java
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@ -20,7 +20,6 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
@ -31,13 +30,10 @@ import java.util.UUID;
import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.slf4j.LoggerFactory.getLogger;
@ContextConfiguration(classes = {MdmHelperConfig.class})
public class MdmReadVirtualizationInterceptorTest extends BaseMdmR4Test {
private static final Logger ourLog = getLogger(MdmReadVirtualizationInterceptorTest.class);
@RegisterExtension
@Autowired
public MdmHelperR4 myMdmHelper;

98
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/interceptor/MdmReadVirtualizationInterceptor.java
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@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR - Master Data Management
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.mdm.interceptor;
import ca.uhn.fhir.context.FhirContext;
@ -8,10 +27,10 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.model.MdmPidTuple;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.mdm.svc.MdmSearchExpansionSvc;
import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -20,6 +39,7 @@ import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.MultimapBuilder;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -69,10 +89,10 @@ public class MdmReadVirtualizationInterceptor<P extends IResourcePersistentId<?>
private DaoRegistry myDaoRegistry;
@Autowired
private MdmSettings myMdmSettings;
private MdmSearchExpansionSvc myMdmSearchExpansionSvc;
@Autowired
private MdmSearchExpansionSvc myMdmSearchExpansionSvc;
private HapiTransactionService myTxService;
@Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED)
public void hook(RequestDetails theRequestDetails, SearchParameterMap theSearchParameterMap) {
@ -86,26 +106,12 @@ public class MdmReadVirtualizationInterceptor<P extends IResourcePersistentId<?>
ListMultimap<String, Integer> candidateResourceIds = extractRemapCandidateResources(theDetails);
ListMultimap<String, ResourceReferenceInfo> candidateReferences = extractRemapCandidateReferences(theDetails);
// Resolve all the resource IDs we've seen that could be MDM candidates,
// and look for MDM links that have these IDs as either the source or the
// golden resource side of the link
Set<IIdType> allIds = new HashSet<>();
candidateResourceIds.keySet().forEach(t -> allIds.add(newIdType(t)));
candidateReferences.keySet().forEach(t -> allIds.add(newIdType(t)));
List<P> sourcePids =
myIdHelperService.getPidsOrThrowException(RequestPartitionId.allPartitions(), List.copyOf(allIds));
Collection<MdmPidTuple<P>> tuples = myMdmLinkDao.resolveGoldenResources(sourcePids);
// Resolve the link PIDs into FHIR IDs
Set<P> allPersistentIds = new HashSet<>();
tuples.forEach(t -> allPersistentIds.add(t.getGoldenPid()));
tuples.forEach(t -> allPersistentIds.add(t.getSourcePid()));
PersistentIdToForcedIdMap<P> persistentIdToFhirIdMap =
myIdHelperService.translatePidsToForcedIds(allPersistentIds);
CandidateMdmLinkedResources<P> candidates =
findCandidateMdmLinkedResources(candidateResourceIds, candidateReferences);
// Loop through each link and figure out whether we need to remap anything
for (MdmPidTuple<P> tuple : tuples) {
Optional<String> sourceIdOpt = persistentIdToFhirIdMap.get(tuple.getSourcePid());
for (MdmPidTuple<P> tuple : candidates.getTuples()) {
Optional<String> sourceIdOpt = candidates.getFhirIdForPersistentId(tuple.getSourcePid());
if (sourceIdOpt.isPresent()) {
String sourceId = sourceIdOpt.get();
@ -114,7 +120,7 @@ public class MdmReadVirtualizationInterceptor<P extends IResourcePersistentId<?>
if (!referencesToRemap.isEmpty()) {
P associatedGoldenResourcePid = tuple.getGoldenPid();
Optional<String> associatedGoldenResourceId =
persistentIdToFhirIdMap.get(associatedGoldenResourcePid);
candidates.getFhirIdForPersistentId(associatedGoldenResourcePid);
if (associatedGoldenResourceId.isPresent()) {
for (ResourceReferenceInfo referenceInfoToRemap : referencesToRemap) {
IBaseReference referenceToRemap = referenceInfoToRemap.getResourceReference();
@ -124,7 +130,7 @@ public class MdmReadVirtualizationInterceptor<P extends IResourcePersistentId<?>
}
// Filter out source resources
Optional<String> targetIdOpt = persistentIdToFhirIdMap.get(tuple.getGoldenPid());
Optional<String> targetIdOpt = candidates.getFhirIdForPersistentId(tuple.getGoldenPid());
if (targetIdOpt.isPresent()) {
Integer filteredIndex = null;
for (int sourceIdResourceIndex : candidateResourceIds.get(sourceId)) {
@ -153,6 +159,31 @@ public class MdmReadVirtualizationInterceptor<P extends IResourcePersistentId<?>
}
}
@Nonnull
private CandidateMdmLinkedResources<P> findCandidateMdmLinkedResources(
ListMultimap<String, Integer> candidateResourceIds,
ListMultimap<String, ResourceReferenceInfo> candidateReferences) {
return myTxService.withSystemRequest().read(() -> {
// Resolve all the resource IDs we've seen that could be MDM candidates,
// and look for MDM links that have these IDs as either the source or the
// golden resource side of the link
Set<IIdType> allIds = new HashSet<>();
candidateResourceIds.keySet().forEach(t -> allIds.add(newIdType(t)));
candidateReferences.keySet().forEach(t -> allIds.add(newIdType(t)));
List<P> sourcePids =
myIdHelperService.getPidsOrThrowException(RequestPartitionId.allPartitions(), List.copyOf(allIds));
Collection<MdmPidTuple<P>> tuples = myMdmLinkDao.resolveGoldenResources(sourcePids);
// Resolve the link PIDs into FHIR IDs
Set<P> allPersistentIds = new HashSet<>();
tuples.forEach(t -> allPersistentIds.add(t.getGoldenPid()));
tuples.forEach(t -> allPersistentIds.add(t.getSourcePid()));
PersistentIdToForcedIdMap<P> persistentIdToFhirIdMap =
myIdHelperService.translatePidsToForcedIds(allPersistentIds);
return new CandidateMdmLinkedResources<>(tuples, persistentIdToFhirIdMap);
});
}
/**
* @return Returns a map where the keys are a typed ID (Patient/ABC) and the values are the index of
* that resource within the {@link IPreResourceShowDetails}
@ -211,6 +242,25 @@ public class MdmReadVirtualizationInterceptor<P extends IResourcePersistentId<?>
* Is the given resource a candidate for virtualization?
*/
private boolean isRemapCandidate(String theResourceType) {
return myMdmSettings.isSupportedMdmType(theResourceType);
return "Patient".equals(theResourceType);
}
private static class CandidateMdmLinkedResources<P extends IResourcePersistentId<?>> {
private final Collection<MdmPidTuple<P>> myTuples;
private final PersistentIdToForcedIdMap<P> myPersistentIdToFhirIdMap;
public CandidateMdmLinkedResources(
Collection<MdmPidTuple<P>> thePidTuples, PersistentIdToForcedIdMap<P> thePersistentIdToForcedIdMap) {
this.myTuples = thePidTuples;
this.myPersistentIdToFhirIdMap = thePersistentIdToForcedIdMap;
}
public Collection<MdmPidTuple<P>> getTuples() {
return myTuples;
}
public Optional<String> getFhirIdForPersistentId(P theSourcePid) {
return myPersistentIdToFhirIdMap.get(theSourcePid);
}
}
}

19
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/svc/MdmSearchExpansionSvc.java
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@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR - Master Data Management
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.mdm.svc;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;