adding metrics (#5301)

* hapi metrics

* step 1

* metrics service

* adding metrics service

* adding documentation

* refactor

* refactoring

* cleanup

* changing

* adding changelog

* some refactoring

* format

* review fixes part 1

* review points

* review fixes

* updates for code review

* updates for code review

* bumping versions

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.9.8-SNAPSHOT</version>
+		 <version>6.9.9-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-bom/pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>6.9.8-SNAPSHOT</version>
+	<version>6.9.9-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
@@ -12,7 +12,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5274-adding-metric-svc-to-mdm.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 5274
+title: "Added a service for generating metrics on mdm links and resources.
+        This includes JPA queries and updated indices.
+    "

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+import org.springframework.stereotype.Repository;
+
+import java.util.List;
+
+@Repository("metricsRepository")
+public interface IMdmLinkJpaMetricsRepository extends JpaRepository<MdmLink, Long>, IHapiFhirJpaRepository {
+
+	@Query("SELECT ml.myMatchResult AS match_result, ml.myLinkSource AS link_source, count(*) AS c "
+			+ "FROM MdmLink ml "
+			+ "WHERE ml.myMdmSourceType = :resourceName "
+			+ "AND ml.myLinkSource in (:linkSource) "
+			+ "AND ml.myMatchResult in (:matchResult) "
+			+ "GROUP BY match_result, link_source "
+			+ "ORDER BY match_result")
+	Object[][] generateMetrics(
+			@Param("resourceName") String theResourceType,
+			@Param("linkSource") List<MdmLinkSourceEnum> theLinkSources,
+			@Param("matchResult") List<MdmMatchResultEnum> theMatchTypes);
+}

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

@@ -0,0 +1,136 @@
+package ca.uhn.fhir.jpa.dao.mdm;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.dao.data.IMdmLinkJpaMetricsRepository;
+import ca.uhn.fhir.mdm.api.BaseMdmMetricSvc;
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.api.params.GenerateMdmMetricsParameters;
+import ca.uhn.fhir.mdm.model.MdmLinkMetrics;
+import ca.uhn.fhir.mdm.model.MdmLinkScoreMetrics;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+import ca.uhn.fhir.mdm.model.MdmResourceMetrics;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.math.BigInteger;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+import javax.persistence.EntityManager;
+import javax.persistence.EntityManagerFactory;
+import javax.persistence.Query;
+
+public class MdmMetricSvcJpaImpl extends BaseMdmMetricSvc {
+
+	private final IMdmLinkJpaMetricsRepository myJpaRepository;
+
+	private final EntityManagerFactory myEntityManagerFactory;
+
+	public MdmMetricSvcJpaImpl(
+			IMdmLinkJpaMetricsRepository theRepository,
+			DaoRegistry theDaoRegistry,
+			EntityManagerFactory theEntityManagerFactory) {
+		super(theDaoRegistry);
+		myJpaRepository = theRepository;
+		myEntityManagerFactory = theEntityManagerFactory;
+	}
+
+	protected MdmLinkMetrics generateLinkMetrics(GenerateMdmMetricsParameters theParameters) {
+		List<MdmLinkSourceEnum> linkSources = theParameters.getLinkSourceFilters();
+		List<MdmMatchResultEnum> matchResults = theParameters.getMatchResultFilters();
+
+		if (linkSources.isEmpty()) {
+			linkSources = Arrays.asList(MdmLinkSourceEnum.values());
+		}
+		if (matchResults.isEmpty()) {
+			matchResults = Arrays.asList(MdmMatchResultEnum.values());
+		}
+
+		Object[][] data = myJpaRepository.generateMetrics(theParameters.getResourceType(), linkSources, matchResults);
+		MdmLinkMetrics metrics = new MdmLinkMetrics();
+		metrics.setResourceType(theParameters.getResourceType());
+		for (Object[] row : data) {
+			MdmMatchResultEnum matchResult = (MdmMatchResultEnum) row[0];
+			MdmLinkSourceEnum source = (MdmLinkSourceEnum) row[1];
+			long count = (Long) row[2];
+			metrics.addMetric(matchResult, source, count);
+		}
+		return metrics;
+	}
+
+	protected MdmLinkScoreMetrics generateLinkScoreMetrics(GenerateMdmMetricsParameters theParameters) {
+		String resourceType = theParameters.getResourceType();
+
+		List<MdmMatchResultEnum> matchResultTypes = theParameters.getMatchResultFilters();
+
+		// if no result type filter, add all result types
+		if (matchResultTypes.isEmpty()) {
+			matchResultTypes = Arrays.asList(MdmMatchResultEnum.values());
+		}
+
+		String sql = "SELECT %s FROM MPI_LINK ml WHERE ml.TARGET_TYPE = :resourceType "
+				+ "AND ml.MATCH_RESULT in (:matchResult)";
+
+		StringBuilder sb = new StringBuilder();
+		sb.append("sum(case when ml.SCORE is null then 1 else 0 end) as B_" + NULL_VALUE);
+
+		for (int i = 0; i < BUCKETS; i++) {
+			double bucket = getBucket(i + 1);
+			sb.append(",\n");
+			if (i == 0) {
+				// score <= .01
+				sb.append(String.format("sum(case when ml.SCORE <= %.2f then 1 else 0 end) as B%d", bucket, i));
+			} else {
+				// score > i/100 && score <= i/100
+				sb.append(String.format(
+						"sum(case when ml.score > %.2f and ml.SCORE <= %.2f then 1 else 0 end) as B%d",
+						getBucket(i), bucket, i));
+			}
+		}
+
+		EntityManager em = myEntityManagerFactory.createEntityManager();
+
+		Query nativeQuery = em.createNativeQuery(String.format(sql, sb.toString()));
+
+		org.hibernate.query.Query<?> hibernateQuery = (org.hibernate.query.Query<?>) nativeQuery;
+
+		hibernateQuery.setParameter("resourceType", resourceType);
+		hibernateQuery.setParameter(
+				"matchResult", matchResultTypes.stream().map(Enum::ordinal).collect(Collectors.toList()));
+
+		List<?> results = hibernateQuery.getResultList();
+
+		em.close();
+
+		MdmLinkScoreMetrics metrics = new MdmLinkScoreMetrics();
+
+		// we only get one row back
+		Object[] row = (Object[]) results.get(0);
+		int length = row.length;
+		for (int i = 0; i < length; i++) {
+			// if there's nothing in the db, these values will all be null
+			BigInteger bi = row[i] != null ? (BigInteger) row[i] : BigInteger.valueOf(0);
+			double bucket = getBucket(i);
+			if (i == 0) {
+				metrics.addScore(NULL_VALUE, bi.longValue());
+			} else if (i == 1) {
+				metrics.addScore(String.format(FIRST_BUCKET, bucket), bi.longValue());
+			} else {
+				metrics.addScore(String.format(NTH_BUCKET, getBucket(i - 1), bucket), bi.longValue());
+			}
+		}
+
+		return metrics;
+	}
+
+	@Transactional
+	@Override
+	public MdmMetrics generateMdmMetrics(GenerateMdmMetricsParameters theParameters) {
+		MdmResourceMetrics resourceMetrics = generateResourceMetrics(theParameters);
+		MdmLinkMetrics linkMetrics = generateLinkMetrics(theParameters);
+		MdmLinkScoreMetrics scoreMetrics = generateLinkScoreMetrics(theParameters);
+
+		MdmMetrics metrics = MdmMetrics.fromSeperableMetrics(resourceMetrics, linkMetrics, scoreMetrics);
+		return metrics;
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/MdmLink.java

@@ -64,7 +64,10 @@ import javax.persistence.UniqueConstraint;
 			@Index(name = "IDX_EMPI_MATCH_TGT_VER", columnList = "MATCH_RESULT, TARGET_PID, VERSION"),
 			// v---- this one
 			@Index(name = "IDX_EMPI_GR_TGT", columnList = "GOLDEN_RESOURCE_PID, TARGET_PID"),
-			@Index(name = "FK_EMPI_LINK_TARGET", columnList = "TARGET_PID")
+			@Index(name = "FK_EMPI_LINK_TARGET", columnList = "TARGET_PID"),
+			// indexes for metrics
+			@Index(name = "IDX_EMPI_TGT_MR_LS", columnList = "TARGET_TYPE, MATCH_RESULT, LINK_SOURCE"),
+			@Index(name = "IDX_EMPI_TGT_MR_SCORE", columnList = "TARGET_TYPE, MATCH_RESULT, SCORE")
 		})
 @Audited
 // This is the table name generated by default by envers, but we set it explicitly for clarity

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -93,6 +93,23 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		init640_after_20230126();
 		init660();
 		init680();
+		init700();
+	}
+
+	protected void init700() {
+		Builder version = forVersion(VersionEnum.V7_0_0);
+
+		// new indices on MdmLink
+		Builder.BuilderWithTableName mdmLinkTable = version.onTable("MPI_LINK");
+
+		mdmLinkTable
+				.addIndex("20230911.1", "IDX_EMPI_TGT_MR_LS")
+				.unique(false)
+				.withColumns("TARGET_TYPE", "MATCH_RESULT", "LINK_SOURCE");
+		mdmLinkTable
+				.addIndex("20230911.2", "IDX_EMPi_TGT_MR_SCore")
+				.unique(false)
+				.withColumns("TARGET_TYPE", "MATCH_RESULT", "SCORE");
 	}
 
 	protected void init680() {

hapi-fhir-jpaserver-elastic-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-hfql/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-ips/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java

@@ -39,7 +39,7 @@ import ca.uhn.fhir.jpa.mdm.svc.MdmLinkUpdaterSvcImpl;
 import ca.uhn.fhir.jpa.mdm.svc.MdmMatchFinderSvcImpl;
 import ca.uhn.fhir.jpa.mdm.svc.MdmMatchLinkSvc;
 import ca.uhn.fhir.jpa.mdm.svc.MdmModelConverterSvcImpl;
-import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
+import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvcImpl;
 import ca.uhn.fhir.jpa.mdm.svc.MdmResourceFilteringSvc;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.CandidateSearcher;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.FindCandidateByEidSvc;
@@ -57,6 +57,7 @@ import ca.uhn.fhir.mdm.api.IMdmLinkQuerySvc;
 import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
 import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
 import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.batch2.MdmBatch2Config;
 import ca.uhn.fhir.mdm.blocklist.svc.IBlockListRuleProvider;
@@ -123,8 +124,8 @@ public class MdmConsumerConfig {
 	}
 
 	@Bean
-	MdmResourceDaoSvc mdmResourceDaoSvc() {
+	IMdmResourceDaoSvc mdmResourceDaoSvc() {
-		return new MdmResourceDaoSvc();
+		return new MdmResourceDaoSvcImpl();
 	}
 
 	@Bean

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/GoldenResourceMergerSvcImpl.java

@@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
 import ca.uhn.fhir.mdm.api.IGoldenResourceMergerSvc;
 import ca.uhn.fhir.mdm.api.IMdmLink;
 import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
 import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
@@ -74,7 +75,7 @@ public class GoldenResourceMergerSvcImpl implements IGoldenResourceMergerSvc {
 	IIdHelperService myIdHelperService;
 
 	@Autowired
-	MdmResourceDaoSvc myMdmResourceDaoSvc;
+	IMdmResourceDaoSvc myMdmResourceDaoSvc;
 
 	@Autowired
 	MdmPartitionHelper myMdmPartitionHelper;

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.mdm.svc.candidate.MatchedGoldenResourceCandidate;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmGoldenResourceFindingSvc;
 import ca.uhn.fhir.mdm.api.IMdmLink;
 import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
@@ -49,7 +50,7 @@ public class MdmEidUpdateService {
 	private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
 
 	@Autowired
-	private MdmResourceDaoSvc myMdmResourceDaoSvc;
+	private IMdmResourceDaoSvc myMdmResourceDaoSvc;
 
 	@Autowired
 	private IMdmLinkSvc myMdmLinkSvc;

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
 import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmLink;
 import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
 import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
@@ -51,7 +52,7 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
 	private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
 
 	@Autowired
-	private MdmResourceDaoSvc myMdmResourceDaoSvc;
+	private IMdmResourceDaoSvc myMdmResourceDaoSvc;
 
 	@Autowired
 	private MdmLinkDaoSvc myMdmLinkDaoSvc;

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImpl.java

@@ -30,6 +30,7 @@ import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
 import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
 import ca.uhn.fhir.mdm.api.IMdmLink;
 import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
@@ -72,7 +73,7 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
 	MdmLinkDaoSvc myMdmLinkDaoSvc;
 
 	@Autowired
-	MdmResourceDaoSvc myMdmResourceDaoSvc;
+	IMdmResourceDaoSvc myMdmResourceDaoSvc;
 
 	@Autowired
 	MdmMatchLinkSvc myMdmMatchLinkSvc;

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java

@@ -19,6 +19,7 @@
  */
 package ca.uhn.fhir.jpa.mdm.svc;
 
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.mdm.models.FindGoldenResourceCandidatesParams;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.CandidateList;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.CandidateStrategyEnum;
@@ -70,6 +71,9 @@ public class MdmMatchLinkSvc {
 	@Autowired
 	private IBlockRuleEvaluationSvc myBlockRuleEvaluationSvc;
 
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
 	@Autowired
 	private IMdmSurvivorshipService myMdmSurvivorshipService;
 
@@ -106,6 +110,8 @@ public class MdmMatchLinkSvc {
 		 * (so that future resources may match to it).
 		 */
 		boolean isResourceBlocked = myBlockRuleEvaluationSvc.isMdmMatchingBlocked(theResource);
+		// we will mark the golden resource special for this
+		theMdmTransactionContext.setIsBlocked(isResourceBlocked);
 
 		if (!isResourceBlocked) {
 			FindGoldenResourceCandidatesParams params =

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmResourceDaoSvcImpl.java

@@ -26,14 +26,15 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.api.MdmConstants;
+import ca.uhn.fhir.mdm.util.MdmSearchParamBuildingUtils;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
-import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -42,10 +43,9 @@ import org.springframework.stereotype.Service;
 
 import java.util.List;
 import java.util.Optional;
-import javax.annotation.Nonnull;
 
 @Service
-public class MdmResourceDaoSvc {
+public class MdmResourceDaoSvcImpl implements IMdmResourceDaoSvc {
 
 	private static final int MAX_MATCHING_GOLDEN_RESOURCES = 1000;
 
@@ -55,6 +55,7 @@ public class MdmResourceDaoSvc {
 	@Autowired
 	IMdmSettings myMdmSettings;
 
+	@Override
 	public DaoMethodOutcome upsertGoldenResource(IAnyResource theGoldenResource, String theResourceType) {
 		IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourceType);
 		RequestDetails requestDetails = new SystemRequestDetails().setRequestPartitionId((RequestPartitionId)
@@ -66,12 +67,7 @@ public class MdmResourceDaoSvc {
 		}
 	}
 
-	/**
+	@Override
-	 * Given a resource, remove its Golden Resource tag.
-	 *
-	 * @param theGoldenResource the {@link IAnyResource} to remove the tag from.
-	 * @param theResourcetype   the type of that resource
-	 */
 	public void removeGoldenResourceTag(IAnyResource theGoldenResource, String theResourcetype) {
 		IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourcetype);
 		RequestDetails requestDetails = new SystemRequestDetails().setRequestPartitionId((RequestPartitionId)
@@ -84,18 +80,22 @@ public class MdmResourceDaoSvc {
 				requestDetails);
 	}
 
+	@Override
 	public IAnyResource readGoldenResourceByPid(IResourcePersistentId theGoldenResourcePid, String theResourceType) {
 		IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourceType);
 		return (IAnyResource) resourceDao.readByPid(theGoldenResourcePid);
 	}
 
+	@Override
 	public Optional<IAnyResource> searchGoldenResourceByEID(String theEid, String theResourceType) {
 		return this.searchGoldenResourceByEID(theEid, theResourceType, null);
 	}
 
+	@Override
 	public Optional<IAnyResource> searchGoldenResourceByEID(
 			String theEid, String theResourceType, RequestPartitionId thePartitionId) {
-		SearchParameterMap map = buildEidSearchParameterMap(theEid, theResourceType);
+		SearchParameterMap map = MdmSearchParamBuildingUtils.buildEidSearchParameterMap(
+				theEid, theResourceType, myMdmSettings.getMdmRules());
 
 		IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourceType);
 		SystemRequestDetails systemRequestDetails = new SystemRequestDetails();
@@ -118,16 +118,4 @@ public class MdmResourceDaoSvc {
 			return Optional.of((IAnyResource) resources.get(0));
 		}
 	}
-
-	@Nonnull
-	private SearchParameterMap buildEidSearchParameterMap(String theEid, String theResourceType) {
-		SearchParameterMap map = new SearchParameterMap();
-		map.setLoadSynchronous(true);
-		map.add(
-				"identifier",
-				new TokenParam(
-						myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType(theResourceType), theEid));
-		map.add("_tag", new TokenParam(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD));
-		return map;
-	}
 }

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByEidSvc.java

@@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
 
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
-import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.IMdmLink;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
 import ca.uhn.fhir.mdm.log.Logs;
 import ca.uhn.fhir.mdm.model.CanonicalEID;
@@ -47,7 +47,7 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder {
 	private EIDHelper myEIDHelper;
 
 	@Autowired
-	private MdmResourceDaoSvc myMdmResourceDaoSvc;
+	private IMdmResourceDaoSvc myMdmResourceDaoSvc;
 
 	@Autowired
 	private MdmLinkDaoSvc myMdmLinkDaoSvc;

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvc.java

@@ -20,7 +20,7 @@
 package ca.uhn.fhir.jpa.mdm.svc.candidate;
 
 import ca.uhn.fhir.jpa.mdm.models.FindGoldenResourceCandidatesParams;
-import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.log.Logs;
 import ca.uhn.fhir.mdm.model.MdmTransactionContext;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
@@ -36,7 +36,7 @@ public class MdmGoldenResourceFindingSvc {
 	private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
 
 	@Autowired
-	private MdmResourceDaoSvc myMdmResourceDaoSvc;
+	private IMdmResourceDaoSvc myMdmResourceDaoSvc;
 
 	@Autowired
 	private FindCandidateByEidSvc myFindCandidateByEidSvc;

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

@@ -98,8 +98,6 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
 		.setValue("555-555-5555");
 	private static final String NAME_GIVEN_FRANK = "Frank";
 
-
-
 	@Autowired
 	protected IFhirResourceDao<Patient> myPatientDao;
 	@Autowired

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

@@ -0,0 +1,172 @@
+package ca.uhn.fhir.jpa.mdm.dao;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
+import ca.uhn.fhir.jpa.dao.data.IMdmLinkJpaMetricsRepository;
+import ca.uhn.fhir.jpa.dao.mdm.MdmMetricSvcJpaImpl;
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
+import ca.uhn.fhir.jpa.mdm.IMdmMetricSvcTest;
+import ca.uhn.fhir.jpa.mdm.helper.MdmLinkHelper;
+import ca.uhn.fhir.jpa.mdm.helper.testmodels.MDMState;
+import ca.uhn.fhir.jpa.mdm.models.GenerateMetricsTestParameters;
+import ca.uhn.fhir.jpa.mdm.models.LinkMetricTestParameters;
+import ca.uhn.fhir.jpa.mdm.models.LinkScoreMetricTestParams;
+import ca.uhn.fhir.jpa.mdm.models.ResourceMetricTestParams;
+import ca.uhn.fhir.jpa.model.dao.JpaPid;
+import ca.uhn.fhir.mdm.api.IMdmMetricSvc;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+import ca.uhn.fhir.mdm.util.MdmResourceUtil;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.BeforeEach;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.test.context.ContextConfiguration;
+
+import javax.persistence.EntityManagerFactory;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.fail;
+
+@ContextConfiguration(classes = {
+	MdmMetricSvcJpaIT.TestConfig.class
+})
+public class MdmMetricSvcJpaIT extends BaseMdmR4Test implements IMdmMetricSvcTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(MdmMetricSvcJpaIT.class);
+
+	@Configuration
+	public static class TestConfig {
+
+		@Autowired
+		@Qualifier("metricsRepository")
+		private IMdmLinkJpaMetricsRepository myJpaRepository;
+
+		@Autowired
+		private DaoRegistry myDaoRegistry;
+
+		@Autowired
+		private EntityManagerFactory myEntityManagerFactory;
+
+		@Autowired
+		private HapiFhirLocalContainerEntityManagerFactoryBean myEntityFactory;
+
+		// this has to be provided via spring, or the
+		// @Transactional barrier is never invoked
+		@Bean
+		IMdmMetricSvc mdmMetricSvc() {
+			return new MdmMetricSvcJpaImpl(
+				myJpaRepository,
+				myDaoRegistry,
+				myEntityManagerFactory
+			);
+		}
+	}
+
+	private final ObjectMapper myObjectMapper = new ObjectMapper();
+
+	@Autowired
+	private MdmLinkHelper myLinkHelper;
+
+	@Autowired
+	private IMdmMetricSvc mySvc;
+
+	@BeforeEach
+	public void before() throws Exception {
+		super.before();
+	}
+
+	@Override
+	public IMdmMetricSvc getMetricsSvc() {
+		return mySvc;
+	}
+
+	@Override
+	public void generateMdmMetricsSetup(GenerateMetricsTestParameters theParameters) {
+		if (StringUtils.isNotBlank(theParameters.getInitialState())) {
+			MDMState<Patient, JpaPid> state = new MDMState<>();
+			state.setInputState(theParameters.getInitialState());
+			myLinkHelper.setup(state);
+
+			// update scores if needed
+			setupScores(theParameters.getScores());
+		}
+	}
+
+	@Override
+	public void generateLinkMetricsSetup(LinkMetricTestParameters theParameters) {
+		ourLog.info(theParameters.getInitialState());
+		if (StringUtils.isNotBlank(theParameters.getInitialState())) {
+			// we can only initialize the state if there is a state to initialize
+			MDMState<Patient, JpaPid> state = new MDMState<>();
+			state.setInputState(theParameters.getInitialState());
+			myLinkHelper.setup(state);
+		}
+	}
+
+	@Override
+	public void generateResourceMetricsSetup(ResourceMetricTestParams theParams) {
+		MDMState<Patient, JpaPid> state = new MDMState<>();
+		String initialState = theParams.getInitialState();
+		if (StringUtils.isNotBlank(initialState)) {
+			state.setInputState(initialState);
+
+			for (String forcedBlockedGRId : theParams.getBlockedResourceGoldenResourceIds()) {
+				Patient gr = new Patient();
+				gr.setActive(true);
+				gr.setId("Patient/" + forcedBlockedGRId);
+				MdmResourceUtil.setMdmManaged(gr);
+				MdmResourceUtil.setGoldenResource(gr);
+				MdmResourceUtil.setGoldenResourceAsBlockedResourceGoldenResource(gr);
+
+				Patient p = createPatient(gr, true, false);
+				state.addParameter(forcedBlockedGRId, p);
+			}
+
+			myLinkHelper.setup(state);
+		}
+	}
+
+	@Override
+	public void generateLinkScoreMetricsSetup(LinkScoreMetricTestParams theParams) {
+		MDMState<Patient, JpaPid> state = new MDMState<>();
+		String initialState = theParams.getInitialState();
+
+		if (StringUtils.isNotBlank(initialState)) {
+			state.setInputState(initialState);
+
+			myLinkHelper.setup(state);
+
+			// update scores if needed
+			setupScores(theParams.getScores());
+		}
+	}
+
+	private void setupScores(List<Double> theParams) {
+		List<MdmLink> links = myMdmLinkDao.findAll();
+		for (int i = 0; i < theParams.size() && i < links.size(); i++) {
+			Double score = theParams.get(i);
+			MdmLink link = links.get(i);
+			link.setScore(score);
+			myMdmLinkDao.save(link);
+		}
+	}
+
+	@Override
+	public String getStringMetrics(MdmMetrics theMetrics) {
+		try {
+			return myObjectMapper.writeValueAsString(theMetrics);
+		} catch (JsonProcessingException ex) {
+			// we've failed anyway - we might as well display the exception
+			fail(ex);
+			return "NOT PARSEABLE!";
+		}
+	}
+}

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

@@ -41,7 +41,7 @@ class MdmLinkUpdaterSvcImplIT extends BaseMdmR4Test {
 	private IMdmLinkUpdaterSvc myMdmLinkUpdaterSvc;
 
 	@Autowired
-	private MdmResourceDaoSvc myMdmResourceDaoSvc;
+	private MdmResourceDaoSvcImpl myMdmResourceDaoSvc;
 
 	@Autowired
 	private MessageHelper myMessageHelper;

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

@@ -7,13 +7,13 @@ import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
+import ca.uhn.fhir.mdm.api.IMdmResourceDaoSvc;
 import ca.uhn.fhir.mdm.util.MdmResourceUtil;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.jupiter.api.AfterEach;
@@ -21,7 +21,6 @@ import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 
@@ -35,7 +34,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 public class MdmResourceDaoSvcTest extends BaseMdmR4Test {
 	private static final String TEST_EID = "TEST_EID";
 	@Autowired
-	MdmResourceDaoSvc myResourceDaoSvc;
+	IMdmResourceDaoSvc myResourceDaoSvc;
 	@Autowired
 	private ISearchParamExtractor mySearchParamExtractor;
 

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu2/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-dstu3/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-r4/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-r4b/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-r5/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/IMdmMetricSvcTest.java

@@ -0,0 +1,177 @@
+package ca.uhn.fhir.jpa.mdm;
+
+import ca.uhn.fhir.jpa.mdm.models.GenerateMetricsTestParameters;
+import ca.uhn.fhir.jpa.mdm.models.LinkMetricTestParameters;
+import ca.uhn.fhir.jpa.mdm.models.LinkScoreMetricTestParams;
+import ca.uhn.fhir.jpa.mdm.models.ResourceMetricTestParams;
+import ca.uhn.fhir.jpa.mdm.util.MdmMetricSvcTestUtil;
+import ca.uhn.fhir.mdm.api.IMdmMetricSvc;
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.api.params.GenerateMdmMetricsParameters;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+import ca.uhn.fhir.mdm.model.MdmResourceMetrics;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.util.Arrays;
+import java.util.Map;
+import java.util.function.Supplier;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+/**
+ * Tests the various metrics returned by IMdmMetricSvc
+ * Because of the way these metrics are broken down in 3 different ways,
+ * these results are tested separately, even though there is a single
+ * entry point.
+ */
+public interface IMdmMetricSvcTest {
+
+	IMdmMetricSvc getMetricsSvc();
+
+	void generateMdmMetricsSetup(GenerateMetricsTestParameters theParameters);
+
+	@Test
+	default void generateMdmMetrics_generalTest_happyPath() {
+		// setup
+		GenerateMetricsTestParameters testParameters = new GenerateMetricsTestParameters();
+		testParameters.setInitialState(MdmMetricSvcTestUtil.OUR_BASIC_STATE);
+		testParameters.setScores(Arrays.asList(0.1, 0.2, 0.3, 0.4));
+
+		generateMdmMetricsSetup(testParameters);
+
+		// test
+		GenerateMdmMetricsParameters parameters = new GenerateMdmMetricsParameters("Patient");
+		MdmMetrics results = getMetricsSvc().generateMdmMetrics(parameters);
+
+		// verify
+		assertNotNull(results);
+		assertEquals("Patient", results.getResourceType());
+		assertEquals(4, results.getGoldenResourcesCount());
+		assertEquals(4, results.getSourceResourcesCount());
+		assertEquals(0, results.getExcludedResources());
+
+		Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> map = results.getMatchTypeToLinkToCountMap();
+		// See OUR_BASIC_STATE
+		assertEquals(3, map.size());
+		for (MdmMatchResultEnum matchResult : new MdmMatchResultEnum[] {
+			MdmMatchResultEnum.MATCH, MdmMatchResultEnum.NO_MATCH, MdmMatchResultEnum.POSSIBLE_MATCH
+		}) {
+			assertTrue(map.containsKey(matchResult));
+			Map<MdmLinkSourceEnum, Long> source2Count = map.get(matchResult);
+			assertNotNull(source2Count);
+			for (MdmLinkSourceEnum ls : MdmLinkSourceEnum.values()) {
+				assertNotNull(source2Count.get(ls));
+			}
+		}
+	}
+
+	void generateLinkMetricsSetup(LinkMetricTestParameters theParameters);
+
+	@ParameterizedTest
+	@MethodSource("ca.uhn.fhir.jpa.mdm.util.MdmMetricSvcTestUtil#linkMetricsParameters")
+	default void test_generateLinkMetrics_multipleInputs(LinkMetricTestParameters theParameters) {
+		// setup
+		generateLinkMetricsSetup(theParameters);
+
+		// all tests use Patient resource type
+		GenerateMdmMetricsParameters parameters = new GenerateMdmMetricsParameters("Patient");
+		for (MdmLinkSourceEnum linkSource : theParameters.getLinkSourceFilters()) {
+			parameters.addLinkSource(linkSource);
+		}
+		for (MdmMatchResultEnum matchResultEnum : theParameters.getMatchFilters()) {
+			parameters.addMatchResult(matchResultEnum);
+		}
+
+		// test
+		MdmMetrics metrics = getMetricsSvc().generateMdmMetrics(parameters);
+
+		// verify
+		assertNotNull(metrics);
+		assertEquals(metrics.getResourceType(), "Patient");
+
+		MdmMetrics expectedMetrics = theParameters.getExpectedMetrics();
+
+		Supplier<String> err = () -> getComparingMetrics(metrics, expectedMetrics);
+
+		Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> actual = metrics.getMatchTypeToLinkToCountMap();
+		Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> expected = expectedMetrics.getMatchTypeToLinkToCountMap();
+		assertEquals(expected, actual, err.get());
+
+		for (MdmMatchResultEnum matchResult : MdmMatchResultEnum.values()) {
+			assertEquals(expected.containsKey(matchResult), actual.containsKey(matchResult), err.get());
+			if (actual.containsKey(matchResult)) {
+				Map<MdmLinkSourceEnum, Long> actualMatch = actual.get(matchResult);
+				Map<MdmLinkSourceEnum, Long> expectedMatch = expected.get(matchResult);
+				assertEquals(expectedMatch, actualMatch, err.get());
+				for (MdmLinkSourceEnum linkSource : MdmLinkSourceEnum.values()) {
+					assertEquals(expectedMatch.get(linkSource), actualMatch.get(linkSource), err.get());
+				}
+			}
+		}
+	}
+
+	void generateResourceMetricsSetup(ResourceMetricTestParams theParams);
+
+	@ParameterizedTest
+	@MethodSource("ca.uhn.fhir.jpa.mdm.util.MdmMetricSvcTestUtil#resourceMetricParameters")
+	default void test_generateResourceMetrics_multipleInputs(ResourceMetricTestParams theParams) {
+		// setup
+		generateResourceMetricsSetup(theParams);
+
+		// test
+		GenerateMdmMetricsParameters parameters = new GenerateMdmMetricsParameters("Patient");
+		MdmResourceMetrics results = getMetricsSvc().generateMdmMetrics(parameters);
+
+		// verify
+		assertNotNull(results);
+		assertEquals("Patient", results.getResourceType());
+		assertEquals(
+				theParams.getExpectedResourceCount(),
+				results.getSourceResourcesCount() + results.getGoldenResourcesCount());
+		assertEquals(theParams.getExpectedBlockedResourceCount(), results.getExcludedResources());
+		assertEquals(theParams.getExpectedGoldenResourceCount(), results.getGoldenResourcesCount());
+	}
+
+	void generateLinkScoreMetricsSetup(LinkScoreMetricTestParams theParams);
+
+	@ParameterizedTest
+	@MethodSource("ca.uhn.fhir.jpa.mdm.util.MdmMetricSvcTestUtil#linkScoreParameters")
+	default void test_generateLinkScoreMetrics_multipleInputs(LinkScoreMetricTestParams theParams) {
+		// setup
+		generateLinkScoreMetricsSetup(theParams);
+
+		GenerateMdmMetricsParameters scoreMetricsParameters = new GenerateMdmMetricsParameters("Patient");
+		for (MdmMatchResultEnum matchType : theParams.getMatchFilter()) {
+			scoreMetricsParameters.addMatchResult(matchType);
+		}
+
+		// test
+		MdmMetrics actualMetrics = getMetricsSvc().generateMdmMetrics(scoreMetricsParameters);
+
+		// verify
+		assertNotNull(actualMetrics);
+		assertEquals("Patient", actualMetrics.getResourceType());
+
+		MdmMetrics expectedMetrics = theParams.getExpectedMetrics();
+
+		Map<String, Long> actual = actualMetrics.getScoreCounts();
+		Map<String, Long> expected = expectedMetrics.getScoreCounts();
+		assertEquals(expected.size(), actual.size());
+		for (String score : expected.keySet()) {
+			assertTrue(actual.containsKey(score), String.format("Score of %s is not in results", score));
+			assertEquals(expected.get(score), actual.get(score), score);
+		}
+	}
+
+	private String getComparingMetrics(MdmMetrics theActual, MdmMetrics theExpected) {
+		return String.format(
+				"\nExpected: \n%s - \nActual: \n%s", getStringMetrics(theExpected), getStringMetrics(theActual));
+	}
+
+	String getStringMetrics(MdmMetrics theMetrics);
+}

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/models/GenerateMetricsTestParameters.java

@@ -0,0 +1,31 @@
+package ca.uhn.fhir.jpa.mdm.models;
+
+import java.util.List;
+
+public class GenerateMetricsTestParameters {
+
+	private String myInitialState;
+
+	/**
+	 * The scores for each link.
+	 * The order should match the order of the
+	 * links listed in initial state.
+	 */
+	private List<Double> myScores;
+
+	public String getInitialState() {
+		return myInitialState;
+	}
+
+	public void setInitialState(String theInitialState) {
+		myInitialState = theInitialState;
+	}
+
+	public List<Double> getScores() {
+		return myScores;
+	}
+
+	public void setScores(List<Double> theScores) {
+		myScores = theScores;
+	}
+}

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/models/LinkMetricTestParameters.java

@@ -0,0 +1,68 @@
+package ca.uhn.fhir.jpa.mdm.models;
+
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class LinkMetricTestParameters {
+	/**
+	 * The initial state (as to be fed into MdmLinkHelper)
+	 */
+	private String myInitialState;
+
+	/**
+	 * The filters for MatchResult
+	 */
+	private List<MdmMatchResultEnum> myMatchFilters;
+
+	/**
+	 * The filters for LinkSource
+	 */
+	private List<MdmLinkSourceEnum> myLinkSourceEnums;
+
+	/**
+	 * The expected metrics to be returned
+	 */
+	private MdmMetrics myExpectedMetrics;
+
+	public String getInitialState() {
+		return myInitialState;
+	}
+
+	public void setInitialState(String theInitialState) {
+		myInitialState = theInitialState;
+	}
+
+	public List<MdmMatchResultEnum> getMatchFilters() {
+		if (myMatchFilters == null) {
+			myMatchFilters = new ArrayList<>();
+		}
+		return myMatchFilters;
+	}
+
+	public void setMatchFilters(List<MdmMatchResultEnum> theMatchFilters) {
+		myMatchFilters = theMatchFilters;
+	}
+
+	public List<MdmLinkSourceEnum> getLinkSourceFilters() {
+		if (myLinkSourceEnums == null) {
+			myLinkSourceEnums = new ArrayList<>();
+		}
+		return myLinkSourceEnums;
+	}
+
+	public void setLinkSourceFilters(List<MdmLinkSourceEnum> theLinkSourceEnums) {
+		myLinkSourceEnums = theLinkSourceEnums;
+	}
+
+	public MdmMetrics getExpectedMetrics() {
+		return myExpectedMetrics;
+	}
+
+	public void setExpectedMetrics(MdmMetrics theExpectedMetrics) {
+		myExpectedMetrics = theExpectedMetrics;
+	}
+}

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/models/LinkScoreMetricTestParams.java

@@ -0,0 +1,60 @@
+package ca.uhn.fhir.jpa.mdm.models;
+
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class LinkScoreMetricTestParams {
+	private String myInitialState;
+
+	private List<MdmMatchResultEnum> myMatchFilter;
+
+	private MdmMetrics myExpectedMetrics;
+
+	/**
+	 * The scores for each link.
+	 * The order should match the order of the
+	 * links listed in initial state.
+	 */
+	private List<Double> myScores;
+
+	public String getInitialState() {
+		return myInitialState;
+	}
+
+	public void setInitialState(String theInitialState) {
+		myInitialState = theInitialState;
+	}
+
+	public MdmMetrics getExpectedMetrics() {
+		return myExpectedMetrics;
+	}
+
+	public void setExpectedMetrics(MdmMetrics theExpectedMetrics) {
+		myExpectedMetrics = theExpectedMetrics;
+	}
+
+	public List<MdmMatchResultEnum> getMatchFilter() {
+		if (myMatchFilter == null) {
+			myMatchFilter = new ArrayList<>();
+		}
+		return myMatchFilter;
+	}
+
+	public void addMatchType(MdmMatchResultEnum theResultEnum) {
+		getMatchFilter().add(theResultEnum);
+	}
+
+	public List<Double> getScores() {
+		if (myScores == null) {
+			myScores = new ArrayList<>();
+		}
+		return myScores;
+	}
+
+	public void setScores(List<Double> theScores) {
+		myScores = theScores;
+	}
+}

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/models/ResourceMetricTestParams.java

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.jpa.mdm.models;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class ResourceMetricTestParams {
+	/**
+	 * The initial state, as consumable by
+	 * MdmLinkHelper.
+	 */
+	private String myInitialState;
+
+	/**
+	 * The list of Golden Resource Ids (in initial state) that should be
+	 * saved as BlockedResources
+	 */
+	private List<String> myBlockedResourceGoldenResourceIds;
+
+	private long myExpectedResourceCount;
+
+	private long myExpectedGoldenResourceCount;
+
+	public String getInitialState() {
+		return myInitialState;
+	}
+
+	public void setInitialState(String theInitialState) {
+		myInitialState = theInitialState;
+	}
+
+	public List<String> getBlockedResourceGoldenResourceIds() {
+		if (myBlockedResourceGoldenResourceIds == null) {
+			myBlockedResourceGoldenResourceIds = new ArrayList<>();
+		}
+		return myBlockedResourceGoldenResourceIds;
+	}
+
+	public void addBlockedResourceGoldenResources(String theBlockedResourceId) {
+		getBlockedResourceGoldenResourceIds().add(theBlockedResourceId);
+	}
+
+	public long getExpectedResourceCount() {
+		return myExpectedResourceCount;
+	}
+
+	public void setExpectedResourceCount(long theExpectedResourceCount) {
+		myExpectedResourceCount = theExpectedResourceCount;
+	}
+
+	public long getExpectedGoldenResourceCount() {
+		return myExpectedGoldenResourceCount;
+	}
+
+	public void setExpectedGoldenResourceCount(long theExpectedGoldenResourceCount) {
+		myExpectedGoldenResourceCount = theExpectedGoldenResourceCount;
+	}
+
+	public long getExpectedBlockedResourceCount() {
+		return getBlockedResourceGoldenResourceIds().size();
+	}
+}

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * This package is for persistence-agnostic mdm tests.
+ * Even though the package is "jpaserver-test-utils", these
+ * classes are not dependent on jpa backed persistence.
+ */
+package ca.uhn.fhir.jpa.mdm;

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/mdm/util/MdmMetricSvcTestUtil.java

@@ -0,0 +1,338 @@
+package ca.uhn.fhir.jpa.mdm.util;
+
+import ca.uhn.fhir.jpa.mdm.models.LinkMetricTestParameters;
+import ca.uhn.fhir.jpa.mdm.models.LinkScoreMetricTestParams;
+import ca.uhn.fhir.jpa.mdm.models.ResourceMetricTestParams;
+import ca.uhn.fhir.mdm.api.BaseMdmMetricSvc;
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+/**
+ * This provides parameter methods for the {@link ca.uhn.fhir.jpa.mdm.IMdmMetricSvcTest}.
+ */
+public class MdmMetricSvcTestUtil {
+
+	public static final String OUR_BASIC_STATE =
+			"""
+					G1, AUTO, MATCH, P1
+					G2, AUTO, MATCH, P2,
+					G3, AUTO, POSSIBLE_MATCH, P3,
+					G4, MANUAL, MATCH, P4
+					G2, AUTO, NO_MATCH, P1
+					G1, MANUAL, NO_MATCH, P2
+					G1, MANUAL, POSSIBLE_MATCH, P3
+				""";
+
+	/**
+	 * Parameters supplied to {@link ca.uhn.fhir.jpa.mdm.IMdmMetricSvcTest#test_generateLinkMetrics_multipleInputs(LinkMetricTestParameters)}
+	 */
+	public static List<LinkMetricTestParameters> linkMetricsParameters() {
+		List<LinkMetricTestParameters> params = new ArrayList<>();
+
+		// 1
+		{
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState(OUR_BASIC_STATE);
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.addMetric(MdmMatchResultEnum.MATCH, MdmLinkSourceEnum.AUTO, 2);
+			metrics.addMetric(MdmMatchResultEnum.MATCH, MdmLinkSourceEnum.MANUAL, 1);
+			metrics.addMetric(MdmMatchResultEnum.NO_MATCH, MdmLinkSourceEnum.AUTO, 1);
+			metrics.addMetric(MdmMatchResultEnum.NO_MATCH, MdmLinkSourceEnum.MANUAL, 1);
+			metrics.addMetric(MdmMatchResultEnum.POSSIBLE_MATCH, MdmLinkSourceEnum.AUTO, 1);
+			metrics.addMetric(MdmMatchResultEnum.POSSIBLE_MATCH, MdmLinkSourceEnum.MANUAL, 1);
+			testParameters.setExpectedMetrics(metrics);
+			params.add(testParameters);
+		}
+
+		// 2
+		{
+			// link source filter
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState(OUR_BASIC_STATE);
+			testParameters.setLinkSourceFilters(Arrays.asList(MdmLinkSourceEnum.AUTO));
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.addMetric(MdmMatchResultEnum.MATCH, MdmLinkSourceEnum.AUTO, 2);
+			metrics.addMetric(MdmMatchResultEnum.NO_MATCH, MdmLinkSourceEnum.AUTO, 1);
+			metrics.addMetric(MdmMatchResultEnum.POSSIBLE_MATCH, MdmLinkSourceEnum.AUTO, 1);
+			testParameters.setExpectedMetrics(metrics);
+			params.add(testParameters);
+		}
+
+		// 3
+		{
+			// match result filter
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState(OUR_BASIC_STATE);
+			testParameters.setMatchFilters(Arrays.asList(MdmMatchResultEnum.MATCH, MdmMatchResultEnum.POSSIBLE_MATCH));
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.addMetric(MdmMatchResultEnum.MATCH, MdmLinkSourceEnum.AUTO, 2);
+			metrics.addMetric(MdmMatchResultEnum.MATCH, MdmLinkSourceEnum.MANUAL, 1);
+			metrics.addMetric(MdmMatchResultEnum.POSSIBLE_MATCH, MdmLinkSourceEnum.AUTO, 1);
+			metrics.addMetric(MdmMatchResultEnum.POSSIBLE_MATCH, MdmLinkSourceEnum.MANUAL, 1);
+			testParameters.setExpectedMetrics(metrics);
+			params.add(testParameters);
+		}
+
+		// 4
+		{
+			// match result and link source filters
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState(OUR_BASIC_STATE);
+			testParameters.setMatchFilters(Arrays.asList(MdmMatchResultEnum.MATCH));
+			testParameters.setLinkSourceFilters(Arrays.asList(MdmLinkSourceEnum.MANUAL));
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.addMetric(MdmMatchResultEnum.MATCH, MdmLinkSourceEnum.MANUAL, 1);
+			testParameters.setExpectedMetrics(metrics);
+			params.add(testParameters);
+		}
+
+		// 5
+		{
+			// no initial state
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState("");
+			MdmMetrics metrics = new MdmMetrics();
+			testParameters.setExpectedMetrics(metrics);
+			params.add(testParameters);
+		}
+
+		// 6
+		{
+			// initial state with filters to omit all values
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState("""
+					G1, AUTO, NO_MATCH, P1
+					G2, MANUAL, MATCH, P2
+				""");
+			testParameters.setMatchFilters(Arrays.asList(MdmMatchResultEnum.MATCH));
+			testParameters.setLinkSourceFilters(Arrays.asList(MdmLinkSourceEnum.AUTO));
+			testParameters.setExpectedMetrics(new MdmMetrics());
+			params.add(testParameters);
+		}
+
+		// 7
+		{
+			// initial state with filters to omit some values
+			LinkMetricTestParameters testParameters = new LinkMetricTestParameters();
+			testParameters.setInitialState("""
+					G1, AUTO, NO_MATCH, P1
+					G2, MANUAL, MATCH, P2
+				""");
+			testParameters.setMatchFilters(Arrays.asList(MdmMatchResultEnum.NO_MATCH));
+			testParameters.setLinkSourceFilters(Arrays.asList(MdmLinkSourceEnum.AUTO));
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.addMetric(MdmMatchResultEnum.NO_MATCH, MdmLinkSourceEnum.AUTO, 1);
+			testParameters.setExpectedMetrics(metrics);
+			params.add(testParameters);
+		}
+
+		return params;
+	}
+
+	/**
+	 * Parameters supplied to {@link ca.uhn.fhir.jpa.mdm.IMdmMetricSvcTest#test_generateResourceMetrics_multipleInputs(ResourceMetricTestParams)}
+	 */
+	public static List<ResourceMetricTestParams> resourceMetricParameters() {
+		List<ResourceMetricTestParams> params = new ArrayList<>();
+
+		// 1
+		{
+			// a mix of golden, regular, and blocked resources
+			ResourceMetricTestParams p = new ResourceMetricTestParams();
+			p.setInitialState(
+					"""
+				G1, AUTO, MATCH, P1
+				G2, AUTO, MATCH, P2
+				G2, AUTO, MATCH, P1,
+				G3, AUTO, MATCH, P3
+			""");
+			p.addBlockedResourceGoldenResources("G2");
+			p.addBlockedResourceGoldenResources("G3");
+			p.setExpectedResourceCount(6);
+			p.setExpectedGoldenResourceCount(3);
+			params.add(p);
+		}
+
+		// 2
+		{
+			// 2 non-golden, 1 golden
+			ResourceMetricTestParams p = new ResourceMetricTestParams();
+			p.setInitialState("""
+				G1, AUTO, MATCH, P1,
+				G1, MANUAL, MATCH, P2
+			""");
+			p.setExpectedResourceCount(3);
+			p.setExpectedGoldenResourceCount(1);
+			params.add(p);
+		}
+
+		// 3
+		{
+			// 2 golden, 1 non-golden
+			ResourceMetricTestParams p = new ResourceMetricTestParams();
+			p.setInitialState("""
+				G1, AUTO, MATCH, P1
+				G2, AUTO, POSSIBLE_DUPLICATE, G1
+			""");
+			p.setExpectedGoldenResourceCount(2);
+			p.setExpectedResourceCount(3);
+			params.add(p);
+		}
+
+		// 4
+		{
+			// 2 golden, 1 blocked, 0 non-golden
+			ResourceMetricTestParams p = new ResourceMetricTestParams();
+			p.setInitialState("""
+				G1, AUTO, POSSIBLE_DUPLICATE, G2
+			""");
+			p.addBlockedResourceGoldenResources("G1");
+			p.setExpectedResourceCount(2);
+			p.setExpectedGoldenResourceCount(2);
+			params.add(p);
+		}
+
+		// 5
+		{
+			// no resources
+			ResourceMetricTestParams p = new ResourceMetricTestParams();
+			p.setInitialState("");
+			params.add(p);
+		}
+
+		return params;
+	}
+
+	/**
+	 * Parameters supplied to {@link ca.uhn.fhir.jpa.mdm.IMdmMetricSvcTest#generateLinkScoreMetricsSetup(LinkScoreMetricTestParams)}
+	 */
+	public static List<LinkScoreMetricTestParams> linkScoreParameters() {
+		List<LinkScoreMetricTestParams> parameters = new ArrayList<>();
+
+		// 1
+		{
+			// score counts
+			LinkScoreMetricTestParams p = new LinkScoreMetricTestParams();
+			p.setInitialState(
+					"""
+				G1, AUTO, MATCH, P1
+				G2, AUTO, POSSIBLE_MATCH, P2,
+				G3, AUTO, POSSIBLE_MATCH, P1
+			""");
+			p.setScores(Arrays.asList(.2D, .2D, .1D));
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.setResourceType("Patient");
+			populateScoreIntoMetrics(p, metrics);
+			p.setExpectedMetrics(metrics);
+			parameters.add(p);
+		}
+
+		// 2
+		{
+			// a null score
+			LinkScoreMetricTestParams p = new LinkScoreMetricTestParams();
+			p.setInitialState("""
+				G1, AUTO, POSSIBLE_MATCH, P1,
+				G2, AUTO, POSSIBLE_MATCH, P2
+			""");
+			p.setScores(Arrays.asList(null, 0.02D));
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.setResourceType("Patient");
+			populateScoreIntoMetrics(p, metrics);
+			p.setExpectedMetrics(metrics);
+			parameters.add(p);
+		}
+
+		// 3
+		{
+			// match type filtering
+			LinkScoreMetricTestParams p = new LinkScoreMetricTestParams();
+			p.setInitialState(
+					"""
+				G1, AUTO, POSSIBLE_MATCH, P1
+				G2, AUTO, MATCH, P2
+				G3, AUTO, POSSIBLE_MATCH, P3
+				G4, AUTO, MATCH, P4
+			""");
+			p.setScores(Arrays.asList(0.4D, 0.4D, 0.1D, 0.3D));
+			p.addMatchType(MdmMatchResultEnum.POSSIBLE_MATCH);
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.setResourceType("Patient");
+			populateScoreIntoMetrics(p, metrics);
+			p.setExpectedMetrics(metrics);
+			parameters.add(p);
+		}
+
+		// 4
+		{
+			// no links
+			LinkScoreMetricTestParams p = new LinkScoreMetricTestParams();
+			p.setInitialState("");
+			MdmMetrics metrics = new MdmMetrics();
+			metrics.setResourceType("Patient");
+			p.setExpectedMetrics(metrics);
+			populateScoreIntoMetrics(p, metrics);
+			parameters.add(p);
+		}
+
+		return parameters;
+	}
+
+	private static void populateScoreIntoMetrics(LinkScoreMetricTestParams p, MdmMetrics metrics) {
+		String initialState = p.getInitialState();
+		Map<Integer, MdmMatchResultEnum> indexToMatchResult = new HashMap<>();
+		if (isNotBlank(initialState)) {
+			String[] states = initialState.split("\n");
+			int len = states.length;
+			for (int i = 0; i < len; i++) {
+				String state = states[i];
+				String[] values = state.split(",");
+				indexToMatchResult.put(i, MdmMatchResultEnum.valueOf(values[2].trim()));
+			}
+		}
+
+		Map<Double, Long> score2Count = new HashMap<>();
+		long nullCount = 0;
+		for (int i = 0; i < p.getScores().size(); i++) {
+			MdmMatchResultEnum matchResult = indexToMatchResult.get(i);
+			// if it's not a filtered value, add it to the expected metrics
+			if (p.getMatchFilter().isEmpty() || p.getMatchFilter().contains(matchResult)) {
+				Double d = p.getScores().get(i);
+				if (d == null) {
+					nullCount++;
+				} else {
+					if (!score2Count.containsKey(d)) {
+						score2Count.put(d, 0L);
+					}
+					score2Count.put(d, score2Count.get(d) + 1);
+				}
+			}
+		}
+		metrics.addScore(BaseMdmMetricSvc.NULL_VALUE, nullCount);
+		for (int i = 0; i < BaseMdmMetricSvc.BUCKETS; i++) {
+			double bucket = (double) Math.round((float) (100 * (i + 1)) / BaseMdmMetricSvc.BUCKETS) / 100;
+			long count = 0;
+			// TODO - do not add it if the corresponding link does not have
+			// the correct MATCH_RESULT value
+			if (score2Count.containsKey(bucket)) {
+				count = score2Count.get(bucket);
+			}
+			if (i == 0) {
+				metrics.addScore(String.format(BaseMdmMetricSvc.FIRST_BUCKET, bucket), count);
+			} else {
+				metrics.addScore(
+						String.format(BaseMdmMetricSvc.NTH_BUCKET, (float) i / BaseMdmMetricSvc.BUCKETS, bucket),
+						count);
+			}
+		}
+	}
+}

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-server-cds-hooks/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/BaseMdmMetricSvc.java

@@ -0,0 +1,94 @@
+package ca.uhn.fhir.mdm.api;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.mdm.api.params.GenerateMdmMetricsParameters;
+import ca.uhn.fhir.mdm.model.MdmResourceMetrics;
+import ca.uhn.fhir.mdm.util.MdmSearchParamBuildingUtils;
+import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+
+public abstract class BaseMdmMetricSvc implements IMdmMetricSvc {
+
+	/**
+	 * Count of numbered buckets.
+	 * There will also be a NULL bucket, so there will be a total
+	 * of BUCKETS + 1 buckets.
+	 */
+	public static final int BUCKETS = 100;
+
+	/**
+	 * The NULL label
+	 */
+	public static final String NULL_VALUE = "NULL";
+
+	/**
+	 * The label for the first bucket
+	 */
+	public static final String FIRST_BUCKET = "x_<_%.2f";
+
+	/**
+	 * The label for the nth bucket (2... buckets)
+	 */
+	public static final String NTH_BUCKET = "%.2f_<_x_<=_%.2f";
+
+	protected final DaoRegistry myDaoRegistry;
+
+	public BaseMdmMetricSvc(DaoRegistry theDaoRegistry) {
+		myDaoRegistry = theDaoRegistry;
+	}
+
+	protected double getBucket(int theBucketId) {
+		return (double) Math.round((float) (100 * theBucketId) / BUCKETS) / 100;
+	}
+
+	protected MdmResourceMetrics generateResourceMetrics(GenerateMdmMetricsParameters theParameters) {
+		String resourceType = theParameters.getResourceType();
+		@SuppressWarnings("rawtypes")
+		IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceType);
+
+		// TODO
+		/*
+		 * We are using 3 different queries to count:
+		 * * all resources
+		 * * all golden resources
+		 * * all blocked resources.
+		 *
+		 * This is inefficient and if we want, we can speed it up with
+		 * a custom query in the future.
+		 */
+		IBundleProvider outcome = null;
+		SearchParameterMap map = null;
+
+		MdmResourceMetrics metrics = new MdmResourceMetrics();
+		metrics.setResourceType(resourceType);
+
+		// find golden resources
+		map = MdmSearchParamBuildingUtils.buildBasicGoldenResourceSearchParameterMap(resourceType);
+		setCountOnly(map);
+		outcome = dao.search(map, new SystemRequestDetails());
+		metrics.setGoldenResourcesCount(outcome.size());
+
+		// find blocked resources
+		map = MdmSearchParamBuildingUtils.buildSearchParameterForBlockedResourceCount(resourceType);
+		setCountOnly(map);
+		outcome = dao.search(map, new SystemRequestDetails());
+		metrics.setExcludedResources(outcome.size());
+
+		// find all resources
+		map = new SearchParameterMap();
+		setCountOnly(map);
+		outcome = dao.search(map, new SystemRequestDetails());
+		metrics.setSourceResourcesCount(outcome.size() - metrics.getGoldenResourcesCount());
+
+		return metrics;
+	}
+
+	private void setCountOnly(SearchParameterMap theMap) {
+		theMap.setCount(0);
+		theMap.setLoadSynchronous(true);
+		theMap.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmMetricSvc.java

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.mdm.api;
+
+import ca.uhn.fhir.mdm.api.params.GenerateMdmMetricsParameters;
+import ca.uhn.fhir.mdm.model.MdmMetrics;
+
+public interface IMdmMetricSvc {
+
+	/**
+	 * Generates metrics on MDM Links.
+	 * Metrics include:
+	 * * breakdowns of counts of MATCH_RESULT types by LINK_SOURCE types.
+	 * * counts of resources of each type
+	 * * a histogram of score 'buckets' with the appropriate counts.
+	 * @param theParameters - Parameters defining resource type of interest,
+	 *                      as well as MatchResult and LinkSource filters.
+	 * @return The metrics in a JSON format.
+	 */
+	MdmMetrics generateMdmMetrics(GenerateMdmMetricsParameters theParameters);
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmResourceDaoSvc.java

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.mdm.api;
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+
+import java.util.Optional;
+
+public interface IMdmResourceDaoSvc {
+	DaoMethodOutcome upsertGoldenResource(IAnyResource theGoldenResource, String theResourceType);
+
+	/**
+	 * Given a resource, remove its Golden Resource tag.
+	 *
+	 * @param theGoldenResource the {@link IAnyResource} to remove the tag from.
+	 * @param theResourcetype   the type of that resource
+	 */
+	void removeGoldenResourceTag(IAnyResource theGoldenResource, String theResourcetype);
+
+	IAnyResource readGoldenResourceByPid(IResourcePersistentId theGoldenResourcePid, String theResourceType);
+
+	Optional<IAnyResource> searchGoldenResourceByEID(String theEid, String theResourceType);
+
+	Optional<IAnyResource> searchGoldenResourceByEID(
+			String theEid, String theResourceType, RequestPartitionId thePartitionId);
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/MdmConstants.java

@@ -34,6 +34,13 @@ public class MdmConstants {
 			"http://hapifhir.io/fhir/NamingSystem/mdm-golden-resource-enterprise-id";
 	public static final String ALL_RESOURCE_SEARCH_PARAM_TYPE = "*";
 
+	/**
+	 * Blocked resource tag info
+	 */
+	public static final String CODE_BLOCKED = "BLOCKED_RESOURCE";
+
+	public static final String CODE_BLOCKED_DISPLAY = "Source Resource is omitted from MDM matching.";
+
 	public static final String FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE =
 			"http://hl7.org/fhir/StructureDefinition/match-grade";
 

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/params/GenerateMdmLinkMetricParameters.java

@@ -0,0 +1,60 @@
+package ca.uhn.fhir.mdm.api.params;
+
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class GenerateMdmLinkMetricParameters {
+
+	/**
+	 * The resource type of interest.
+	 * Must be provided!
+	 */
+	private final String myResourceType;
+
+	/**
+	 * The MDM MatchResult types of interest.
+	 * Specified MatchResults will be included.
+	 * If none are specified, all will be included.
+	 */
+	private List<MdmMatchResultEnum> myMatchResultFilters;
+
+	/**
+	 * The MDM Link values of interest.
+	 * Specified LinkSources will be included.
+	 * If none are specified, all are included.
+	 */
+	private List<MdmLinkSourceEnum> myLinkSourceFilters;
+
+	public GenerateMdmLinkMetricParameters(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public List<MdmMatchResultEnum> getMatchResultFilters() {
+		if (myMatchResultFilters == null) {
+			myMatchResultFilters = new ArrayList<>();
+		}
+		return myMatchResultFilters;
+	}
+
+	public void addMatchResultFilter(MdmMatchResultEnum theMdmMatchResultEnum) {
+		getMatchResultFilters().add(theMdmMatchResultEnum);
+	}
+
+	public List<MdmLinkSourceEnum> getLinkSourceFilters() {
+		if (myLinkSourceFilters == null) {
+			myLinkSourceFilters = new ArrayList<>();
+		}
+		return myLinkSourceFilters;
+	}
+
+	public void addLinkSourceFilter(MdmLinkSourceEnum theLinkSource) {
+		getLinkSourceFilters().add(theLinkSource);
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/params/GenerateMdmMetricsParameters.java

@@ -0,0 +1,69 @@
+package ca.uhn.fhir.mdm.api.params;
+
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class GenerateMdmMetricsParameters {
+
+	/**
+	 * We only allow finding metrics by resource type
+	 */
+	private final String myResourceType;
+
+	/**
+	 * The MDM MatchResult types of interest.
+	 * Specified MatchResults will be included.
+	 * If none are specified, all will be included.
+	 */
+	private List<MdmMatchResultEnum> myMatchResultFilters;
+
+	/**
+	 * The MDM Link values of interest.
+	 * Specified LinkSources will be included.
+	 * If none are specified, all are included.
+	 */
+	private List<MdmLinkSourceEnum> myLinkSourceFilters;
+
+	public GenerateMdmMetricsParameters(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public List<MdmMatchResultEnum> getMatchResultFilters() {
+		if (myMatchResultFilters == null) {
+			myMatchResultFilters = new ArrayList<>();
+		}
+		return myMatchResultFilters;
+	}
+
+	public void addMatchResult(MdmMatchResultEnum theMdmMatchResultEnum) {
+		getMatchResultFilters().add(theMdmMatchResultEnum);
+	}
+
+	public List<MdmLinkSourceEnum> getLinkSourceFilters() {
+		if (myLinkSourceFilters == null) {
+			myLinkSourceFilters = new ArrayList<>();
+		}
+		return myLinkSourceFilters;
+	}
+
+	public void addLinkSource(MdmLinkSourceEnum theLinkSource) {
+		getLinkSourceFilters().add(theLinkSource);
+	}
+
+	//	public GenerateMdmLinkMetricParameters toLinkMetricParams() {
+	//
+	//	}
+	//
+	//	public GenerateMdmResourceMetricsParameters toResourceMetricParams() {
+	//
+	//	}
+	//
+
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/params/GenerateMdmResourceMetricsParameters.java

@@ -0,0 +1,17 @@
+package ca.uhn.fhir.mdm.api.params;
+
+public class GenerateMdmResourceMetricsParameters {
+
+	/**
+	 * We only allow finding metrics by resource type
+	 */
+	private final String myResourceType;
+
+	public GenerateMdmResourceMetricsParameters(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/params/GenerateScoreMetricsParameters.java

@@ -0,0 +1,39 @@
+package ca.uhn.fhir.mdm.api.params;
+
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class GenerateScoreMetricsParameters {
+	/**
+	 * The resource type of interest.
+	 */
+	private final String myResourceType;
+
+	/**
+	 * MatchResult types to filter for.
+	 * Specified MatchResults will be included.
+	 * If none specified, all will be included.
+	 */
+	private List<MdmMatchResultEnum> myMatchTypeFilters;
+
+	public GenerateScoreMetricsParameters(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public List<MdmMatchResultEnum> getMatchTypes() {
+		if (myMatchTypeFilters == null) {
+			myMatchTypeFilters = new ArrayList<>();
+		}
+		return myMatchTypeFilters;
+	}
+
+	public void addMatchType(MdmMatchResultEnum theMatchType) {
+		getMatchTypes().add(theMatchType);
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/model/MdmLinkMetrics.java

@@ -0,0 +1,52 @@
+package ca.uhn.fhir.mdm.model;
+
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class MdmLinkMetrics {
+	/**
+	 * The resource type to which these metrics apply.
+	 */
+	private String myResourceType;
+
+	/**
+	 * A mapping of MatchType -> LinkSource -> count.
+	 * Eg:
+	 * MATCH
+	 * 		AUTO    - 2
+	 * 	 	MANUAL  - 1
+	 * NO_MATCH
+	 *      AUTO    - 1
+	 *      MANUAL  - 3
+	 */
+	private Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> myMatchTypeToLinkToCountMap;
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> getMatchTypeToLinkToCountMap() {
+		if (myMatchTypeToLinkToCountMap == null) {
+			myMatchTypeToLinkToCountMap = new HashMap<>();
+		}
+		return myMatchTypeToLinkToCountMap;
+	}
+
+	public void addMetric(
+			MdmMatchResultEnum theMdmMatchResultEnum, MdmLinkSourceEnum theLinkSourceEnum, long theCount) {
+		Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> map = getMatchTypeToLinkToCountMap();
+
+		if (!map.containsKey(theMdmMatchResultEnum)) {
+			map.put(theMdmMatchResultEnum, new HashMap<>());
+		}
+		Map<MdmLinkSourceEnum, Long> lsToCountMap = map.get(theMdmMatchResultEnum);
+		lsToCountMap.put(theLinkSourceEnum, theCount);
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/model/MdmLinkScoreMetrics.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.mdm.model;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+public class MdmLinkScoreMetrics {
+
+	private String myResourceType;
+
+	/**
+	 * Map of Score:Count
+	 * Scores are typically Doubles. But we cast to string because
+	 * Score is not a non-null field, and so "NULL" is a value.
+	 */
+	private Map<String, Long> myScoreCounts;
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public Map<String, Long> getScoreCounts() {
+		if (myScoreCounts == null) {
+			myScoreCounts = new LinkedHashMap<>();
+		}
+		return myScoreCounts;
+	}
+
+	public void addScore(String theScore, Long theCount) {
+		getScoreCounts().put(theScore, theCount);
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/model/MdmMetrics.java

@@ -0,0 +1,132 @@
+package ca.uhn.fhir.mdm.model;
+
+import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
+import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.model.api.IModelJson;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+public class MdmMetrics extends MdmResourceMetrics implements IModelJson {
+
+	@JsonProperty("resourceType")
+	private String myResourceType;
+
+	/**
+	 * A mapping of MatchType -> LinkSource -> count.
+	 * Eg:
+	 * MATCH
+	 * 		AUTO    - 2
+	 * 	 	MANUAL  - 1
+	 * NO_MATCH
+	 *      AUTO    - 1
+	 *      MANUAL  - 3
+	 */
+	@JsonProperty("matchResult2linkSource2count")
+	private Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> myMatchTypeToLinkToCountMap;
+
+	/**
+	 * Score buckets (in brackets of 0.01 size, and null) to counts.
+	 */
+	@JsonProperty("scoreCounts")
+	private Map<String, Long> myScoreCounts;
+
+	/**
+	 * The number of golden resources.
+	 */
+	@JsonProperty("goldenResources")
+	private long myGoldenResourcesCount;
+
+	/**
+	 * The number of source resources.
+	 */
+	@JsonProperty("sourceResources")
+	private long mySourceResourcesCount;
+
+	/**
+	 * The number of excluded resources.
+	 * These are necessarily a subset of both
+	 * GoldenResources and SourceResources
+	 * (as each Blocked resource will still generate
+	 * a GoldenResource)
+	 */
+	@JsonProperty("excludedResources")
+	private long myExcludedResources;
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> getMatchTypeToLinkToCountMap() {
+		if (myMatchTypeToLinkToCountMap == null) {
+			myMatchTypeToLinkToCountMap = new HashMap<>();
+		}
+		return myMatchTypeToLinkToCountMap;
+	}
+
+	public void addMetric(
+			MdmMatchResultEnum theMdmMatchResultEnum, MdmLinkSourceEnum theLinkSourceEnum, long theCount) {
+		Map<MdmMatchResultEnum, Map<MdmLinkSourceEnum, Long>> map = getMatchTypeToLinkToCountMap();
+
+		if (!map.containsKey(theMdmMatchResultEnum)) {
+			map.put(theMdmMatchResultEnum, new HashMap<>());
+		}
+		Map<MdmLinkSourceEnum, Long> lsToCountMap = map.get(theMdmMatchResultEnum);
+		lsToCountMap.put(theLinkSourceEnum, theCount);
+	}
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public long getGoldenResourcesCount() {
+		return myGoldenResourcesCount;
+	}
+
+	public void setGoldenResourcesCount(long theGoldenResourcesCount) {
+		myGoldenResourcesCount = theGoldenResourcesCount;
+	}
+
+	public long getSourceResourcesCount() {
+		return mySourceResourcesCount;
+	}
+
+	public void setSourceResourcesCount(long theSourceResourcesCount) {
+		mySourceResourcesCount = theSourceResourcesCount;
+	}
+
+	public long getExcludedResources() {
+		return myExcludedResources;
+	}
+
+	public void setExcludedResources(long theExcludedResources) {
+		myExcludedResources = theExcludedResources;
+	}
+
+	public Map<String, Long> getScoreCounts() {
+		if (myScoreCounts == null) {
+			myScoreCounts = new LinkedHashMap<>();
+		}
+		return myScoreCounts;
+	}
+
+	public void addScore(String theScore, Long theCount) {
+		getScoreCounts().put(theScore, theCount);
+	}
+
+	public static MdmMetrics fromSeperableMetrics(
+			MdmResourceMetrics theMdmResourceMetrics,
+			MdmLinkMetrics theLinkMetrics,
+			MdmLinkScoreMetrics theLinkScoreMetrics) {
+		MdmMetrics metrics = new MdmMetrics();
+		metrics.setResourceType(theMdmResourceMetrics.getResourceType());
+		metrics.setExcludedResources(theMdmResourceMetrics.getExcludedResources());
+		metrics.setGoldenResourcesCount(theMdmResourceMetrics.getGoldenResourcesCount());
+		metrics.setSourceResourcesCount(theMdmResourceMetrics.getSourceResourcesCount());
+		metrics.myMatchTypeToLinkToCountMap = theLinkMetrics.getMatchTypeToLinkToCountMap();
+		metrics.myScoreCounts = theLinkScoreMetrics.getScoreCounts();
+		return metrics;
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/model/MdmResourceMetrics.java

@@ -0,0 +1,60 @@
+package ca.uhn.fhir.mdm.model;
+
+public class MdmResourceMetrics {
+
+	/**
+	 * The resource type to which these metrics apply.
+	 */
+	private String myResourceType;
+
+	/**
+	 * The number of golden resources.
+	 */
+	private long myGoldenResourcesCount;
+
+	/**
+	 * The number of source resources.
+	 */
+	private long mySourceResourcesCount;
+
+	/**
+	 * The number of excluded resources.
+	 * These are necessarily a subset of both
+	 * GoldenResources and SourceResources
+	 * (as each Blocked resource will still generate
+	 * a GoldenResource)
+	 */
+	private long myExcludedResources;
+
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public long getGoldenResourcesCount() {
+		return myGoldenResourcesCount;
+	}
+
+	public void setGoldenResourcesCount(long theGoldenResourcesCount) {
+		myGoldenResourcesCount = theGoldenResourcesCount;
+	}
+
+	public long getSourceResourcesCount() {
+		return mySourceResourcesCount;
+	}
+
+	public void setSourceResourcesCount(long theSourceResourcesCount) {
+		mySourceResourcesCount = theSourceResourcesCount;
+	}
+
+	public long getExcludedResources() {
+		return myExcludedResources;
+	}
+
+	public void setExcludedResources(long theExcludedResources) {
+		myExcludedResources = theExcludedResources;
+	}
+}

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/model/MdmTransactionContext.java

@@ -49,6 +49,12 @@ public class MdmTransactionContext {
 
 	private String myResourceType;
 
+	/**
+	 * Whether or not the currently processed resource is a 'blocked resource'.
+	 * This will only be set on matching.
+	 */
+	private boolean myIsBlockedResource;
+
 	private List<IMdmLink> myMdmLinkEvents = new ArrayList<>();
 
 	public TransactionLogMessages getTransactionLogMessages() {
@@ -111,4 +117,12 @@ public class MdmTransactionContext {
 	public void setMdmLinks(List<IMdmLink> theMdmLinkEvents) {
 		myMdmLinkEvents = theMdmLinkEvents;
 	}
+
+	public void setIsBlocked(boolean theIsBlocked) {
+		myIsBlockedResource = theIsBlocked;
+	}
+
+	public boolean getIsBlocked() {
+		return myIsBlockedResource;
+	}
 }

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java

@@ -116,6 +116,14 @@ public class GoldenResourceHelper {
 		MdmResourceUtil.setMdmManaged(newGoldenResource);
 		MdmResourceUtil.setGoldenResource(newGoldenResource);
 
+		// TODO - on updating links, if resolving a link, this should go away?
+		// blocked resource's golden resource will be marked special
+		// they are not part of MDM matching algorithm (will not link to other resources)
+		// but other resources can link to them
+		if (theMdmTransactionContext.getIsBlocked()) {
+			MdmResourceUtil.setGoldenResourceAsBlockedResourceGoldenResource(newGoldenResource);
+		}
+
 		// add the partition id to the new resource
 		newGoldenResource.setUserData(
 				Constants.RESOURCE_PARTITION_ID,

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/MdmResourceUtil.java

@@ -132,6 +132,24 @@ public final class MdmResourceUtil {
 				MdmConstants.DISPLAY_GOLDEN_REDIRECT);
 	}
 
+	/**
+	 * Adds the BLOCKED tag to the golden resource.
+	 * Because this is called *before* a resource is saved,
+	 * we must add a new system/code combo to it
+	 * @param theBaseResource
+	 * @return
+	 */
+	public static IBaseResource setGoldenResourceAsBlockedResourceGoldenResource(IBaseResource theBaseResource) {
+		IBaseCoding tag = theBaseResource.getMeta().addTag();
+		tag.setSystem(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS);
+		tag.setCode(MdmConstants.CODE_BLOCKED);
+		tag.setDisplay(MdmConstants.CODE_BLOCKED_DISPLAY);
+		tag.setUserSelected(false);
+		tag.setVersion("1");
+
+		return theBaseResource;
+	}
+
 	/**
 	 * WARNING: This code may _look_ like it replaces in place a code of a tag, but this DOES NOT ACTUALLY WORK!. In reality what will
 	 * happen is a secondary tag will be created with the same system. the only way to actually remove a tag from a resource

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/MdmSearchParamBuildingUtils.java

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.mdm.util;
+
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.mdm.api.MdmConstants;
+import ca.uhn.fhir.mdm.rules.json.MdmRulesJson;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+
+public class MdmSearchParamBuildingUtils {
+
+	private static final String IDENTIFIER = "identifier";
+
+	private static final String TAG = "_tag";
+
+	/**
+	 * Builds a search parameter map that can be used to find the
+	 * golden resources associated with MDM blocked resources (ie, those
+	 * resources that were omitted from MDM matching).
+	 */
+	public static SearchParameterMap buildSearchParameterForBlockedResourceCount(String theResourceType) {
+		SearchParameterMap map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		TokenAndListParam tagsToSearch = new TokenAndListParam();
+		tagsToSearch.addAnd(new TokenParam(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD));
+		tagsToSearch.addAnd(new TokenParam(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_BLOCKED));
+
+		map.add(TAG, tagsToSearch);
+		return map;
+	}
+
+	/**
+	 * Creates a SearchParameterMap used for searching for golden resources
+	 * by EID specifically.
+	 */
+	public static SearchParameterMap buildEidSearchParameterMap(
+			String theEid, String theResourceType, MdmRulesJson theMdmRules) {
+		SearchParameterMap map = buildBasicGoldenResourceSearchParameterMap(theEid);
+		map.add(IDENTIFIER, new TokenParam(theMdmRules.getEnterpriseEIDSystemForResourceType(theResourceType), theEid));
+		return map;
+	}
+
+	/**
+	 * Creates a SearchParameterMap that can be used to find golden resources.
+	 */
+	public static SearchParameterMap buildBasicGoldenResourceSearchParameterMap(String theResourceType) {
+		SearchParameterMap map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add(TAG, new TokenParam(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD));
+		return map;
+	}
+}

hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/util/MdmResourceUtilTest.java

@@ -1,11 +1,21 @@
 package ca.uhn.fhir.mdm.util;
 
+import ca.uhn.fhir.mdm.api.MdmConstants;
+import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.Patient;
 import org.junit.jupiter.api.Test;
 
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
 import static org.hamcrest.CoreMatchers.equalTo;
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 class MdmResourceUtilTest {
 
@@ -20,4 +30,28 @@ class MdmResourceUtilTest {
 
 		assertThat(hasGoldenRecordTag, is(equalTo(false)));
 	}
+
+	@Test
+	public void testSetGoldenAndBlockedResource() {
+		// setup
+		Patient patient = new Patient();
+		patient.setActive(true);
+
+		// test
+		Patient changed = (Patient) MdmResourceUtil.setGoldenResourceAsBlockedResourceGoldenResource(
+			MdmResourceUtil.setGoldenResource(patient)
+		);
+
+		// verify
+		assertNotNull(changed);
+		List<Coding> tags = changed.getMeta().getTag();
+		Set<String> codes = new HashSet<>();
+		codes.add(MdmConstants.CODE_BLOCKED);
+		codes.add(MdmConstants.CODE_GOLDEN_RECORD);
+		assertEquals(2, tags.size());
+		for (Coding code : tags) {
+			assertEquals(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, code.getSystem());
+			assertTrue(codes.contains(code.getCode()));
+		}
+	}
 }

hapi-fhir-server-openapi/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-serviceloaders/hapi-fhir-caching-api/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<artifactId>hapi-fhir-serviceloaders</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<artifactId>hapi-fhir-serviceloaders</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>
@@ -21,7 +21,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-caching-api</artifactId>
-			<version>6.9.8-SNAPSHOT</version>
+			<version>6.9.9-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>

hapi-fhir-serviceloaders/hapi-fhir-caching-guava/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<artifactId>hapi-fhir-serviceloaders</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-serviceloaders/hapi-fhir-caching-testing/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<artifactId>hapi-fhir</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../../pom.xml</relativePath>
 	</parent>

hapi-fhir-serviceloaders/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<artifactId>hapi-deployable-pom</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml

@@ -5,7 +5,7 @@
    <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>6.9.8-SNAPSHOT</version>
+      <version>6.9.9-SNAPSHOT</version>
 
       <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
    </parent>

hapi-fhir-spring-boot/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-sql-migrate/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage-batch2-jobs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage-batch2-test-utilities/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage-batch2/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage-cr/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage-mdm/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage-test-utilities/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-storage/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-structures-dstu2.1/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-structures-dstu2/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-structures-dstu3/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.9.8-SNAPSHOT</version>
+		<version>6.9.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>