Add basic skeleton of MDM expansion

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

@@ -33,11 +33,11 @@ import java.util.List;
 @Repository
 public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
 	@Modifying
-	@Query("DELETE FROM MdmLink f WHERE myGoldenResourcePid = :pid OR mySourcePid = :pid")
+	@Query("DELETE FROM MdmLink f WHERE f.myGoldenResourcePid = :pid OR f.mySourcePid = :pid")
 	int deleteWithAnyReferenceToPid(@Param("pid") Long thePid);
 
 	@Modifying
-	@Query("DELETE FROM MdmLink f WHERE (myGoldenResourcePid = :pid OR mySourcePid = :pid) AND myMatchResult <> :matchResult")
+	@Query("DELETE FROM MdmLink f WHERE (f.myGoldenResourcePid = :pid OR f.mySourcePid = :pid) AND f.myMatchResult <> :matchResult")
 	int deleteWithAnyReferenceToPidAndMatchResultNot(@Param("pid") Long thePid, @Param("matchResult") MdmMatchResultEnum theMatchResult);
 
 	@Query("SELECT ml2.myGoldenResourcePid, ml2.mySourcePid FROM MdmLink ml2 " +
@@ -51,4 +51,14 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
 			"AND hrl.myTargetResourceType='Patient'" +
 		")")
 	List<List<Long>> expandPidsFromGroupPidGivenMatchResult(@Param("groupPid") Long theGroupPid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
+
+	@Query("SELECT ml.myGoldenResourcePid, ml.mySourcePid " +
+		"FROM MdmLink ml " +
+		"INNER JOIN MdmLink ml2 " +
+		"on ml.myGoldenResourcePid=ml2.myGoldenResourcePid " +
+		"WHERE ml2.mySourcePid=:sourcePid " +
+		"AND ml2.myMatchResult=:matchResult " +
+		"AND ml.myMatchResult=:matchResult")
+	List<List<Long>> expandPidsBySourcePidAndMatchResult(@Param("sourcePid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java

@@ -380,6 +380,29 @@ public class IdHelperService {
 		}
 	}
 
+	/**
+	 *
+	 * Given a set of PIDs, return a set of public FHIR Resource IDs.
+	 * This function will resolve a forced ID if it resolves, and if it fails to resolve to a forced it, will just return the pid
+	 * Example:
+	 * Let's say we have Patient/1(pid == 1), Patient/pat1 (pid == 2), Patient/3 (pid == 3), their pids would resolve as follows:
+	 *
+	 * [1,2,3] -> ["1","pat1","3"]
+	 *
+	 * @param thePids The Set of pids you would like to resolve to external FHIR Resource IDs.
+	 * @return A Set of strings representing the FHIR IDs of the pids.
+	 */
+	public Set<String> translatePidsToFhirResourceIds(Set<Long> thePids) {
+		Map<Long, Optional<String>> pidToForcedIdMap = translatePidsToForcedIds(thePids);
+
+		//If the result of the translation is an empty optional, it means there is no forced id, and we can use the PID as the resource ID.
+		Set<String> resolvedResourceIds = pidToForcedIdMap.entrySet().stream()
+			.map(entry -> entry.getValue().isPresent() ? entry.getValue().get() : entry.getKey().toString())
+			.collect(Collectors.toSet());
+
+		return resolvedResourceIds;
+
+	}
 	public Map<Long, Optional<String>> translatePidsToForcedIds(Set<Long> thePids) {
 		Map<Long, Optional<String>> retVal = new HashMap<>(myMemoryCacheService.getAllPresent(MemoryCacheService.CacheEnum.FORCED_ID, thePids));
 

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

@@ -0,0 +1,88 @@
+package ca.uhn.fhir.jpa.dao.mdm;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 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%
+ */
+
+import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+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 java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+@Service
+public class MdmLinkExpandSvc {
+	private static final Logger ourLog = LoggerFactory.getLogger(MdmLinkExpandSvc.class);
+
+	@Autowired
+	private IMdmLinkDao myMdmLinkDao;
+	@Autowired
+	private IdHelperService myIdHelperService;
+
+	/**
+	 *  Given a source resource, perform MDM expansion and return all the resource IDs of all resources that are
+	 *  MDM-Matched to this resource.
+	 *
+	 * @param theResource The resource to MDM-Expand
+	 * @return A set of strings representing the FHIR IDs of the expanded resources.
+	 */
+	public Set<String> expandMdmBySourceResource(IBaseResource theResource) {
+		return expandMdmBySourceResourceId(theResource.getIdElement());
+	}
+
+	/**
+	 *  Given a resource ID of a source resource, perform MDM expansion and return all the resource IDs of all resources that are
+	 *  MDM-Matched to this resource.
+	 *
+	 * @param theId The Resource ID of the resource to MDM-Expand
+	 * @return A set of strings representing the FHIR ids of the expanded resources.
+	 */
+	public Set<String> expandMdmBySourceResourceId(IIdType theId) {
+		Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
+		return expandMdmBySourceResourcePid(pidOrThrowException);
+	}
+
+	/**
+	 *  Given a PID of a source resource, perform MDM expansion and return all the resource IDs of all resources that are
+	 *  MDM-Matched to this resource.
+	 *
+	 * @param theSourceResourcePid The PID of the resource to MDM-Expand
+	 * @return A set of strings representing the FHIR ids of the expanded resources.
+	 */
+	public Set<String> expandMdmBySourceResourcePid(Long theSourceResourcePid) {
+		List<List<Long>> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
+		Set<Long> flattenedPids = new HashSet<>();
+		goldenPidSourcePidTuples.forEach(flattenedPids::addAll);
+
+		Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
+		return resourceIds;
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/helper/SearchParamHelper.java

@@ -0,0 +1,60 @@
+package ca.uhn.fhir.jpa.search.helper;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@Service
+public class SearchParamHelper {
+
+	@Autowired
+	private FhirContext myFhirContext;
+
+
+	public Collection<RuntimeSearchParam> getPatientSearchParamsForResourceType(String theResourceType) {
+		RuntimeResourceDefinition runtimeResourceDefinition = myFhirContext.getResourceDefinition(theResourceType);
+		Map<String, RuntimeSearchParam> searchParams = new HashMap<>();
+
+		RuntimeSearchParam  patientSearchParam = runtimeResourceDefinition.getSearchParam("patient");
+		if (patientSearchParam != null) {
+			searchParams.put(patientSearchParam.getName(), patientSearchParam);
+
+		}
+		RuntimeSearchParam  subjectSearchParam = runtimeResourceDefinition.getSearchParam("subject");
+		if (subjectSearchParam != null) {
+			searchParams.put(subjectSearchParam.getName(), subjectSearchParam);
+		}
+
+		List<RuntimeSearchParam> compartmentSearchParams = getPatientCompartmentRuntimeSearchParams(runtimeResourceDefinition);
+		compartmentSearchParams.forEach(param -> searchParams.put(param.getName(), param));
+
+		return searchParams.values();
+	}
+
+	/**
+	 * Search the resource definition for a compartment named 'patient' and return its related Search Parameter.
+	 */
+	public List<RuntimeSearchParam> getPatientCompartmentRuntimeSearchParams(RuntimeResourceDefinition runtimeResourceDefinition) {
+		List<RuntimeSearchParam> patientSearchParam = new ArrayList<>();
+		List<RuntimeSearchParam> searchParams = runtimeResourceDefinition.getSearchParamsForCompartmentName("Patient");
+		return searchParams;
+//		if (searchParams == null || searchParams.size() == 0) {
+//			String errorMessage = String.format("Resource type [%s] is not eligible for this type of export, as it contains no Patient compartment, and no `patient` or `subject` search parameter", myResourceType);
+//			throw new IllegalArgumentException(errorMessage);
+//		} else if (searchParams.size() == 1) {
+//			patientSearchParam = searchParams.get(0);
+//		} else {
+//			String errorMessage = String.format("Resource type [%s] is not eligible for Group Bulk export, as we are unable to disambiguate which patient search parameter we should be searching by.", myResourceType);
+//			throw new IllegalArgumentException(errorMessage);
+//		}
+//		return patientSearchParam;
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

@@ -2635,6 +2635,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	@CoverageIgnore
 	@Override
 	public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
+		//TODO GGG TRY TO JUST AUTO_PASS HERE AND SEE WHAT HAPPENS.
 		invokeRunnableForUnitTest();
 
 		if (isNotBlank(theValueSetUrl)) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChain.java

@@ -68,6 +68,7 @@ public class JpaValidationSupportChain extends ValidationSupportChain {
 	public void postConstruct() {
 		addValidationSupport(myDefaultProfileValidationSupport);
 		addValidationSupport(myJpaValidationSupport);
+		//TODO MAKE SURE THAT THIS IS BEING CAL
 		addValidationSupport(myTerminologyService);
 		addValidationSupport(new SnapshotGeneratingValidationSupport(myFhirContext));
 		addValidationSupport(new InMemoryTerminologyServerValidationSupport(myFhirContext));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -112,7 +112,8 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		};
 
 		retVal.setDriver(new org.h2.Driver());
-		retVal.setUrl("jdbc:h2:mem:testdb_r4");
+		retVal.setUrl("jdbc:h2:file:/home/tadgh/smile/hapi-fhir/testdb_r4.db");
+//		retVal.setUrl("jdbc:h2:mem:testdb_r4");
 		retVal.setMaxWaitMillis(30000);
 		retVal.setUsername("");
 		retVal.setPassword("");

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java

@@ -182,7 +182,6 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
 		Patient patient = (Patient) outcome.getResource();
 		patient.setId(outcome.getId());
 		return patient;
-		
 	}
 
 	@Nonnull

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvcTest.java

@@ -2,15 +2,26 @@ package ca.uhn.fhir.jpa.mdm.dao;
 
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
 import ca.uhn.fhir.mdm.rules.json.MdmRulesJson;
 import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
 import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.util.TestUtil;
+import org.hl7.fhir.r4.model.Patient;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.stream.Collectors;
+
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.in;
 import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.isIn;
 import static org.hamcrest.Matchers.notNullValue;
 import static org.hamcrest.Matchers.nullValue;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -48,4 +59,47 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
 		assertEquals(rules.getVersion(), newLink.getVersion());
 	}
 
+	@Test
+	public void testExpandPidsWorks() {
+
+		Patient golden = createGoldenPatient();
+
+		//Create 10 linked patients.
+		List<MdmLink> mdmLinks = new ArrayList<>();
+		for (int i = 0; i < 10; i++) {
+			mdmLinks.add(createPatientAndLinkTo(golden.getIdElement().getIdPartAsLong(), MdmMatchResultEnum.MATCH));
+		}
+
+		//Now lets connect a few as just POSSIBLE_MATCHes and ensure they aren't returned.
+		for (int i = 0 ; i < 5; i++) {
+			createPatientAndLinkTo(golden.getIdElement().getIdPartAsLong(), MdmMatchResultEnum.POSSIBLE_MATCH);
+		}
+
+		List<Long> expectedExpandedPids = mdmLinks.stream().map(MdmLink::getSourcePid).collect(Collectors.toList());
+
+		//SUT
+		List<List<Long>> lists = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(mdmLinks.get(0).getSourcePid(), MdmMatchResultEnum.MATCH);
+
+		assertThat(lists, hasSize(10));
+
+		lists.stream()
+			.forEach(pair -> {
+					assertThat(pair.get(0), is(equalTo(golden.getIdElement().getIdPartAsLong())));
+					assertThat(pair.get(1), is(in(expectedExpandedPids)));
+				});
+	}
+
+	private MdmLink createPatientAndLinkTo(Long thePatientPid, MdmMatchResultEnum theMdmMatchResultEnum) {
+		Patient patient = createPatient();
+
+		MdmLink mdmLink = myMdmLinkDaoSvc.newMdmLink();
+		mdmLink.setLinkSource(MdmLinkSourceEnum.MANUAL);
+		mdmLink.setMatchResult(theMdmMatchResultEnum);
+		mdmLink.setCreated(new Date());
+		mdmLink.setUpdated(new Date());
+		mdmLink.setGoldenResourcePid(thePatientPid);
+		mdmLink.setSourcePid(myIdHelperService.getPidOrNull(patient));
+		MdmLink saved= myMdmLinkDao.save(mdmLink);
+		return saved;
+	}
 }

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

@@ -16,6 +16,8 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.List;
+
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.core.StringContains.containsString;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -49,6 +51,8 @@ public class MdmExpungeTest extends BaseMdmR4Test {
 		saveLink(mdmLink);
 	}
 
+
+
 	@Test
 	public void testUninterceptedDeleteRemovesMdmReference() {
 		assertEquals(1, myMdmLinkDao.count());

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaR4Config.java

@@ -68,6 +68,7 @@ public class TestJpaR4Config extends BaseJavaConfigR4 {
 
 		retVal.setDriver(new org.h2.Driver());
 		retVal.setUrl("jdbc:h2:mem:testdb_r4");
+//		retVal.setUrl("jdbc:h2:file:/home/tadgh/smile/hapi-fhir/testdb_r4.db");
 		retVal.setMaxWaitMillis(10000);
 		retVal.setUsername("");
 		retVal.setPassword("");