Merge pull request #2872 from hapifhir/issue-2871-enhance-mdm-expansion

Add MDM expansion by golden pid

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java

@@ -75,6 +75,7 @@ public enum VersionEnum {
 	V5_4_1,
 	V5_4_2,
 	V5_5_0,
+
 	;
 
 	public static VersionEnum latestVersion() {

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2871-enhance-mdm-expansion.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2871
+title: "Modified the behaviour of the `:mdm` param qualifier. Previously, it used to only resolve IDs if the resource ID was a source resource.
+Now, MDM expansion will work if you pass it the ID of a golden resource instead."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IMdmLinkDao.java

@@ -67,4 +67,7 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
 		"AND ml.myMatchResult=:matchResult")
 	List<MdmPidTuple> expandPidsBySourcePidAndMatchResult(@Param("sourcePid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
 
+	@Query("SELECT ml.myGoldenResourcePid as goldenPid, ml.mySourcePid as sourcePid FROM MdmLink ml WHERE ml.myGoldenResourcePid = :goldenPid and ml.myMatchResult = :matchResult")
+	List<MdmPidTuple> expandPidsByGoldenResourcePidAndMatchResult(@Param("goldenPid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkExpandSvc.java

@@ -25,15 +25,13 @@ import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
 import ca.uhn.fhir.mdm.log.Logs;
 import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import java.util.ArrayList;
+import javax.annotation.Nonnull;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -82,14 +80,50 @@ public class MdmLinkExpandSvc {
 	public Set<String> expandMdmBySourceResourcePid(Long theSourceResourcePid) {
 		ourLog.debug("About to expand source resource with PID {}", theSourceResourcePid);
 		List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
+		return flattenPidTuplesToSet(theSourceResourcePid, goldenPidSourcePidTuples);
+	}
+
+	/**
+	 *  Given a PID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
+	 *  MDM-Matched to this golden resource.
+	 *
+	 * @param theGoldenResourcePid The PID of the golden resource to MDM-Expand.
+	 * @return A set of strings representing the FHIR ids of the expanded resources.
+	 */
+	public Set<String> expandMdmByGoldenResourceId(Long theGoldenResourcePid) {
+		ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
+		List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
+		return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
+	}
+
+
+	/**
+	 *  Given a resource ID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
+	 *  MDM-Matched to this golden resource.
+	 *
+	 * @param theGoldenResourcePid The resource ID of the golden resource to MDM-Expand.
+	 * @return A set of strings representing the FHIR ids of the expanded resources.
+	 */
+	public Set<String> expandMdmByGoldenResourcePid(Long theGoldenResourcePid) {
+		ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
+		List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
+		return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
+	}
+	public Set<String> expandMdmByGoldenResourceId(IdDt theId) {
+		ourLog.debug("About to expand golden resource with golden resource id {}", theId);
+		Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
+		return expandMdmByGoldenResourcePid(pidOrThrowException);
+	}
+
+	@Nonnull
+	private Set<String> flattenPidTuplesToSet(Long initialPid, List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples) {
 		Set<Long> flattenedPids = new HashSet<>();
 		goldenPidSourcePidTuples.forEach(tuple -> {
 			flattenedPids.add(tuple.getSourcePid());
 			flattenedPids.add(tuple.getGoldenPid());
 		});
 		Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
-		ourLog.debug("Pid {} has been expanded to [{}]", theSourceResourcePid, String.join(",", resourceIds));
+		ourLog.debug("Pid {} has been expanded to [{}]", initialPid, String.join(",", resourceIds));
 		return resourceIds;
 	}
-
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java

@@ -76,8 +76,16 @@ public class MdmSearchExpandingInterceptor {
 			if (iQueryParameterType instanceof ReferenceParam) {
 				ReferenceParam refParam = (ReferenceParam) iQueryParameterType;
 				if (refParam.isMdmExpand()) {
-					ourLog.debug("Found a reference parameter to expand: {}", refParam.toString());
+					ourLog.debug("Found a reference parameter to expand: {}", refParam);
+					//First, attempt to expand as a source resource.
 					Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(refParam.getValue()));
+
+					// If we failed, attempt to expand as a golden resource
+					if (expandedResourceIds.isEmpty()) {
+							expandedResourceIds =  myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
+					}
+
+					//Rebuild the search param list.
 					if (!expandedResourceIds.isEmpty()) {
 						ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
 						toRemove.add(refParam);

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSearchExpandingInterceptorIT.java

@@ -2,14 +2,18 @@ package ca.uhn.fhir.jpa.mdm.interceptor;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
 import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
 import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.mdm.api.MdmConstants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.ReferenceOrListParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
+import org.elasticsearch.common.collect.Set;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
@@ -21,6 +25,8 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
 
+import java.util.List;
+
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.is;
@@ -73,6 +79,19 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
 		myDaoConfig.setAllowMdmExpansion(true);
 		search = myObservationDao.search(searchParameterMap);
 		assertThat(search.size(), is(equalTo(4)));
+		List<MdmLink> all = myMdmLinkDao.findAll();
+		Long goldenPid = all.get(0).getGoldenResourcePid();
+		IIdType goldenId = myIdHelperService.translatePidIdToForcedId(myFhirContext, "Patient", new ResourcePersistentId(goldenPid));
+		//Verify that expansion by the golden resource id resolves down to everything its links have.
+
+		SearchParameterMap goldenSpMap = new SearchParameterMap();
+		goldenSpMap.setLoadSynchronous(true);
+		ReferenceOrListParam goldenReferenceOrListParam = new ReferenceOrListParam();
+		goldenReferenceOrListParam.addOr(new ReferenceParam(goldenId).setMdmExpand(true));
+		goldenSpMap.add(Observation.SP_SUBJECT, goldenReferenceOrListParam);
+
+		search = myObservationDao.search(goldenSpMap);
+		assertThat(search.size(), is(equalTo(4)));
 	}
 
 	@Test