AccessionRefs can be manually re-linked, but are automatically cleared

- Aspect on delete Accession sets AccessionRef#accession to null

src/main/java/org/genesys/catalog/service/DatasetService.java

@@ -15,9 +15,13 @@
  */
 package org.genesys.catalog.service;
 
+import java.io.IOException;
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+import java.util.UUID;
+
 import org.genesys.catalog.exceptions.NotFoundElement;
-import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.model.dataset.DatasetCreator;
 import org.genesys.catalog.model.dataset.DatasetLocation;
@@ -27,18 +31,14 @@ import org.genesys.filerepository.InvalidRepositoryFileDataException;
 import org.genesys.filerepository.InvalidRepositoryPathException;
 import org.genesys.filerepository.NoSuchRepositoryFileException;
 import org.genesys.filerepository.model.RepositoryFile;
-import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionRef;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.web.multipart.MultipartFile;
 
-import java.io.IOException;
-import java.util.List;
-import java.util.Set;
-import java.util.UUID;
-
 /**
  * The Interface DatasetService.
  */
@@ -262,8 +262,19 @@ public interface DatasetService {
 	 */
 	List<Object[]> lastPublished();
 
+	/**
+	 * Rematch dataset accessions for all datasets.
+	 */
 	void rematchDatasetAccessions();
 
+	/**
+	 * Rematch dataset accessions.
+	 *
+	 * @param dataset the dataset
+	 * @return the dataset
+	 */
+	Dataset rematchDatasetAccessions(Dataset dataset);
+
 	/**
 	 * Create DatasetCreator for Dataset.
 	 *
@@ -415,4 +426,12 @@ public interface DatasetService {
 	 */
 	DatasetLocation updateLocation(Dataset dataset, DatasetLocation input) throws NotFoundElement;
 
+	/**
+	 * Clear accession references across all Datasets for specified accessions. 
+	 *
+	 * @param accessions the accessions
+	 * @return the int
+	 */
+	int clearAccessionRefs(Collection<Accession> accessions);
+
 }

src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java

@@ -23,23 +23,25 @@ import java.io.IOException;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
-import com.querydsl.core.types.Predicate;
+
 import org.apache.commons.lang.StringUtils;
 import org.genesys.blocks.security.service.CustomAclService;
 import org.genesys.catalog.exceptions.InvalidApiUsageException;
 import org.genesys.catalog.exceptions.NotFoundElement;
 import org.genesys.catalog.model.Partner;
-import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys.catalog.model.dataset.Dataset;
+import org.genesys.catalog.model.dataset.DatasetCreator;
+import org.genesys.catalog.model.dataset.DatasetLocation;
 import org.genesys.catalog.model.dataset.DatasetVersions;
 import org.genesys.catalog.model.dataset.QDataset;
-import org.genesys.catalog.model.dataset.*;
 import org.genesys.catalog.model.filters.DatasetFilter;
 import org.genesys.catalog.model.traits.Descriptor;
 import org.genesys.catalog.persistence.dataset.DatasetCreatorRepository;
@@ -55,7 +57,7 @@ import org.genesys.filerepository.service.RepositoryService;
 import org.genesys2.server.model.PublishState;
 import org.genesys2.server.model.UserRole;
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.security.SecurityUtils;
 import org.genesys2.server.service.DownloadService;
@@ -64,16 +66,23 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.dao.ConcurrencyFailureException;
 import org.springframework.dao.DataIntegrityViolationException;
-import org.springframework.data.domain.*;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageImpl;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort;
 import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Isolation;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.multipart.MultipartFile;
 
 import com.google.common.collect.Lists;
 import com.querydsl.core.BooleanBuilder;
+import com.querydsl.core.types.Predicate;
 
 
 /**
@@ -145,7 +154,7 @@ public class DatasetServiceImpl implements DatasetService {
 		dataset.setCrops(source.getCrops());
 
 		if (source.getAccessionRefs() != null && !source.getAccessionRefs().isEmpty()) {
-			dataset.setAccessionRefs(lookupMatchingAccessions(new HashSet<>(source.getAccessionRefs())));
+			dataset.setAccessionRefs(lookupMatchingAccessions(source.getAccessionRefs()));
 		}
 
 		copyDescriptors(dataset, source.getDescriptors());
@@ -193,7 +202,7 @@ public class DatasetServiceImpl implements DatasetService {
 		LOG.info("Update AccessionIdentifiers. Input dataset: {}, input accessionRefs {}", dataset, accessionRefs);
 		dataset = loadDataset(dataset);
 		dataset.getAccessionRefs().clear();
-		dataset.setAccessionRefs(lookupMatchingAccessions(new HashSet<>(accessionRefs)));
+		dataset.setAccessionRefs(lookupMatchingAccessions(accessionRefs));
 		return lazyLoad(datasetRepository.save(dataset));
 	}
 
@@ -466,7 +475,7 @@ public class DatasetServiceImpl implements DatasetService {
 			throw new NotFoundElement("Dataset doesn't exist");
 		}
 		loadedDataset.setState(PublishState.DRAFT);
-		loadedDataset.setAccessionRefs(lookupMatchingAccessions(new HashSet<>(accessionRefs)));
+		loadedDataset.setAccessionRefs(lookupMatchingAccessions(accessionRefs));
 		return lazyLoad(datasetRepository.save(loadedDataset));
 	}
 
@@ -768,6 +777,7 @@ public class DatasetServiceImpl implements DatasetService {
 	 * Looking for matching Accession and then sets that to AccessionRef
 	 *
 	 * @param accessionRefs the accessionRefs
+	 *
 	 * @return accessionRefs with matching accessions from Genesys
 	 */
 	private Set<AccessionRef> lookupMatchingAccessions(final Set<AccessionRef> accessionRefs) {
@@ -776,20 +786,20 @@ public class DatasetServiceImpl implements DatasetService {
 		
 		LOG.info("Found {} matches for {} identifiers", foundAccessions.size(), accessionRefs.size());
 		
-		accessionRefs.forEach(accei -> {
+		accessionRefs.forEach(ref -> {
 			Accession foundAccession = foundAccessions.stream().filter(a -> {
-				return StringUtils.equalsIgnoreCase(a.getInstCode(), accei.getInstCode())
+				return StringUtils.equalsIgnoreCase(a.getInstCode(), ref.getInstCode())
 						&& (
 							// when DOI provided
-							(accei.getDoi() != null && a.getDoi() != null && StringUtils.equals(a.getDoi(), accei.getDoi()))
+							(ref.getDoi() != null && a.getDoi() != null && StringUtils.equals(a.getDoi(), ref.getDoi()))
 							// OR when without DOI
 							||
-							(StringUtils.equalsIgnoreCase(a.getAccessionNumber(), accei.getAcceNumb()) && StringUtils.equalsIgnoreCase(a.getGenus(), accei.getGenus()))
+							(StringUtils.equalsIgnoreCase(a.getAccessionNumber(), ref.getAcceNumb()) && StringUtils.equalsIgnoreCase(a.getGenus(), ref.getGenus()))
 						);
 			}).findFirst().orElse(null);
-			accei.setAccession(foundAccession);
+			ref.setAccession(foundAccession);
 			if (foundAccession == null) {
-				LOG.debug("No match for {}", accei);
+				LOG.debug("No match for {}", ref);
 			}
 		});
 
@@ -799,14 +809,43 @@ public class DatasetServiceImpl implements DatasetService {
 	
 	@Override
 	@Transactional(readOnly = false)
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
 	public void rematchDatasetAccessions() {
 		datasetRepository.findAll().forEach(dataset -> {
-			LOG.warn("Linking {} accessions with dataset {}", dataset.getAccessionCount(), dataset.getId());
-			dataset.setAccessionRefs(lookupMatchingAccessions(new HashSet<>(dataset.getAccessionRefs())));
-			datasetRepository.save(dataset);
+			rematchDatasetAccessions(dataset);
 		});
 	}
-
+	
+	@Override
+	@Transactional(readOnly = false)
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#dataset, 'write')")
+	public Dataset rematchDatasetAccessions(Dataset dataset) {
+		dataset = datasetRepository.findByUuid(dataset.getUuid());
+		LOG.warn("Linking {} accessions with dataset {}", dataset.getAccessionCount(), dataset.getId());
+		dataset.setAccessionRefs(lookupMatchingAccessions(dataset.getAccessionRefs()));
+		return datasetRepository.save(dataset);	
+	}
+
+	@Override
+	@Transactional(readOnly = false, propagation = Propagation.REQUIRED, isolation = Isolation.READ_UNCOMMITTED)
+	public int clearAccessionRefs(Collection<Accession> accessions) {
+		Set<UUID> uuids = accessions.stream().map(a -> a.getUuid()).collect(Collectors.toSet());
+		final Iterable<Dataset> datasets = datasetRepository.findAll(dataset.accessionRefs.any().accession.in(accessions));
+
+		AtomicInteger updates = new AtomicInteger(0);
+		datasets.forEach(dataset -> {
+			dataset.getAccessionRefs().stream()
+				// filter for matching accessions
+				.filter(ref -> ref.getAccession() != null && uuids.contains(ref.getAccession().getUuid()))
+				// clear accession reference
+				.forEach(ref -> {
+					updates.incrementAndGet();
+					ref.setAccession(null);
+				});
+		});
+		datasetRepository.save(datasets);
+		return updates.get();
+	}
 
 	/**
 	 * {@inheritDoc}

src/main/java/org/genesys2/server/model/genesys/AccessionData.java

@@ -501,23 +501,9 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 	public String getInstCode() {
 		return this.instituteCode;
 	}
-	
 
 	// FIXME This seems a bit of a hack
 	public boolean getSgsv() {
 		return this.duplSiteStr != null && this.duplSiteStr.contains("NOR051");
 	}
-
-	// TODO Check if needed
-	public AccessionRef toAccessionRef(){
-		AccessionRef res = new AccessionRef();
-		res.setInstCode(getInstCode());
-		res.setGenus(getGenus());
-		res.setDoi(getDoi());
-		res.setAcceNumb(getAccessionNumber());
-		res.setSpecies(getTaxonomy().getSpecies());
-		res.setAccession((Accession) this);
-
-		return res;
-	}
 }

src/main/java/org/genesys2/server/model/genesys/AccessionRef.java

@@ -68,6 +68,23 @@ public class AccessionRef implements AccessionIdentifier3, Serializable {
 	@JsonView({ JsonViews.Public.class })
 	private Accession accession;
 
+	public AccessionRef() {
+	}
+
+	public AccessionRef(Accession accession) {
+		this.instCode = accession.getInstitute().getCode();
+		this.acceNumb = accession.getAccessionNumber();
+		this.genus = accession.getTaxonomy().getGenus();
+		this.doi = accession.getDoi();
+		this.accession = accession;
+	}
+
+	public AccessionRef(String instCode, String acceNumb, String genus, String doi) {
+		this.instCode = instCode;
+		this.acceNumb = acceNumb;
+		this.genus = genus;
+		this.doi = doi;
+	}
 
 	/**
 	 * Gets the doi.
@@ -271,7 +288,7 @@ public class AccessionRef implements AccessionIdentifier3, Serializable {
 		}
 		return true;
 	}
-	
+
 	@Override
 	public String toString() {
 		return "AccessionRef " + instCode + " " + acceNumb + " " + genus;

src/main/java/org/genesys2/server/model/impl/Subset.java

@@ -49,7 +49,6 @@ import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import com.fasterxml.jackson.annotation.JsonView;
 
-// TODO: Auto-generated Javadoc
 /**
  * The Class Subset.
  */
@@ -99,7 +98,7 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 			indexes = { @Index(columnList = "subsetId, instCode, acceNumb"), @Index(columnList = "subsetId, genus") })
 	@Field(type = FieldType.Object)
 	@JsonView({ JsonViews.Public.class })
-	private List<AccessionRef> accessionRefs;
+	private Set<AccessionRef> accessionRefs;
 
 	/** The accession count. */
 	@Column(name = "accession_count", nullable = false)
@@ -276,7 +275,7 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	 *
 	 * @return the accessionRefs
 	 */
-	public List<AccessionRef> getAccessionRefs() {
+	public Set<AccessionRef> getAccessionRefs() {
 		return accessionRefs;
 	}
 
@@ -285,7 +284,7 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	 *
 	 * @param accessionRefs the new accessionRefs
 	 */
-	public void setAccessionRefs(List<AccessionRef> accessions) {
+	public void setAccessionRefs(Set<AccessionRef> accessions) {
 		this.accessionRefs = accessions;
 	}
 

src/main/java/org/genesys2/server/persistence/AccessionRepositoryCustom.java

@@ -33,6 +33,8 @@ public interface AccessionRepositoryCustom {
 
 	List<AccessionData> findActiveAndHistoric(Collection<UUID> accessionUuids);
 
+	List<Accession> find(Collection<UUID> accessionUuids);
+
 	List<Accession> find(List<Accession> accessions);
 
 	List<Accession> findById(List<? extends AccessionIdentifier3> identifiers);

src/main/java/org/genesys2/server/persistence/AccessionRepositoryCustomImpl.java

@@ -45,6 +45,7 @@ import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.IncorrectResultSizeDataAccessException;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.support.Querydsl;
@@ -54,6 +55,8 @@ import org.springframework.transaction.annotation.Transactional;
 import com.querydsl.core.types.dsl.PathBuilder;
 import com.querydsl.core.types.dsl.PathBuilderFactory;
 import com.querydsl.jpa.JPQLQuery;
+import com.querydsl.jpa.impl.JPAQuery;
+import com.querydsl.jpa.impl.JPAQueryFactory;
 
 @Repository
 @Transactional(readOnly = true)
@@ -61,6 +64,9 @@ public class AccessionRepositoryCustomImpl implements AccessionRepositoryCustom,
 	public static final Logger LOG = LoggerFactory.getLogger(AccessionRepositoryCustomImpl.class);
 	private static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[] {};
 
+	@Autowired
+	private JPAQueryFactory jpaQueryFactory;
+	
 	@PersistenceContext
 	private EntityManager em;
 
@@ -265,6 +271,15 @@ public class AccessionRepositoryCustomImpl implements AccessionRepositoryCustom,
 
 		return activeAndHistoric;
 	}
+	
+	@Override
+	public List<Accession> find(Collection<UUID> accessionUuids) {
+		if (accessionUuids.isEmpty()) {
+			return Collections.emptyList();
+		}
+		JPAQuery<Accession> query = jpaQueryFactory.selectFrom(QAccession.accession).distinct().where(QAccession.accession.accessionId.uuid.in(accessionUuids));
+		return query.fetch();
+	}
 
 	@Override
 	public List<Accession> findAll(AccessionFilter filter, Pageable page) {

src/main/java/org/genesys2/server/service/SubsetService.java

@@ -16,13 +16,13 @@
 
 package org.genesys2.server.service;
 
+import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
 
 import org.genesys.catalog.exceptions.NotFoundElement;
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Subset;
 import org.genesys2.server.model.impl.SubsetCreator;
@@ -242,4 +242,24 @@ public interface SubsetService {
     List<SubsetCreator> autocompleteCreators(String text);
 
 
+	/**
+	 * Rematch subset accessions across all Subsets.
+	 */
+	void rematchSubsetAccessions();
+
+	/**
+	 * Rematch subset accessions for a Subset
+	 *
+	 * @param subset the subset
+	 * @return the subset
+	 */
+	Subset rematchSubsetAccessions(Subset subset);
+
+	/**
+	 * Clear accession references across all Subsets for specified accessions.
+	 *
+	 * @param accessions the accessions
+	 * @return the int
+	 */
+	int clearAccessionRefs(Collection<Accession> accessions);
 }

src/main/java/org/genesys2/server/service/impl/SubsetServiceImpl.java

@@ -16,13 +16,19 @@
 
 package org.genesys2.server.service.impl;
 
+import static org.genesys2.server.model.impl.QSubsetCreator.subsetCreator;
+
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
-import com.querydsl.core.types.Predicate;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
 
 import org.apache.commons.lang3.StringUtils;
 import org.genesys.catalog.exceptions.InvalidApiUsageException;
@@ -49,19 +55,20 @@ import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.ConcurrencyFailureException;
 import org.springframework.data.domain.Page;
-import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.PageImpl;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
 import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Isolation;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 import com.querydsl.core.BooleanBuilder;
-
-import static org.genesys2.server.model.impl.QSubsetCreator.subsetCreator;
+import com.querydsl.core.types.Predicate;
 
 /**
  * The Class SubsetServiceImpl.
@@ -145,7 +152,7 @@ public class SubsetServiceImpl implements SubsetService {
 	 * @param target the target
 	 * @param list the subset accessions
 	 */
-	private void copyAccessions(final Subset target, final List<AccessionRef> list) {
+	private void copyAccessions(final Subset target, final Set<AccessionRef> list) {
 		if ((list == null) || (list.size() == 0)) {
 			if (target.getAccessionRefs() != null)
 				target.getAccessionRefs().clear();
@@ -154,11 +161,11 @@ public class SubsetServiceImpl implements SubsetService {
 
 		if (target.getAccessionRefs() != null && !target.getAccessionRefs().isEmpty()) {
 			target.getAccessionRefs().clear();
-			target.getAccessionRefs().addAll(list.stream().distinct().collect(Collectors.toList()));
 		} else {
-			target.setAccessionRefs(list.stream().distinct().collect(Collectors.toList()));
+			target.setAccessionRefs(new HashSet<>());
 		}
 
+		target.getAccessionRefs().addAll(list);
 	}
 
 	/**
@@ -270,10 +277,10 @@ public class SubsetServiceImpl implements SubsetService {
 	 */
 	@Override
 	@Transactional
-	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#subset, 'WRITE')")
-	public Subset delete(final Subset subset) {
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#input, 'DELETE')")
+	public Subset delete(final Subset input) {
+		final Subset subset = loadSubset(input);
 		subsetRepository.delete(subset);
-		subset.setId(null);
 		return subset;
 	}
 
@@ -293,7 +300,8 @@ public class SubsetServiceImpl implements SubsetService {
 		final Set<UUID> uuidsToRemove = accessions.stream().map(AccessionData::getUuid).collect(Collectors.toSet());
 
 		// Keep accessions that are not in the list
-		subset.setAccessionRefs(subset.getAccessionRefs().stream().filter(accessionId -> !uuidsToRemove.contains(accessionId.getAccession().getUuid())).collect(Collectors.toList()));
+		subset.setAccessionRefs(subset.getAccessionRefs().stream().filter(accessionId -> !uuidsToRemove.contains(accessionId.getAccession().getUuid())).collect(Collectors
+			.toSet()));
 
 		subset.setState(PublishState.DRAFT);
 
@@ -310,15 +318,15 @@ public class SubsetServiceImpl implements SubsetService {
 		LOG.info("Add accessions to Subset. Input accessions {}", input);
 		final Subset subset = loadSubset(input);
 
-		final List<AccessionData> accessions = accessionRepository.findActiveAndHistoric(accessionsUuids);
+		final List<Accession> accessions = accessionRepository.find(accessionsUuids);
 
 		final Set<UUID> currentAccessions = subset.getAccessionRefs().stream().map(AccessionRef::getAccession).map(Accession::getUuid).collect(Collectors.toSet());
 
-		for (AccessionData accession : accessions) {
+		for (Accession accession : accessions) {
 			if (currentAccessions.contains(accession.getUuid())) {
 				LOG.warn("Current Subset already contains accession, ignoring");
 			} else {
-				subset.getAccessionRefs().add(accession.toAccessionRef());
+				subset.getAccessionRefs().add(new AccessionRef(accession));
 				currentAccessions.add(accession.getUuid());
 			}
 		}
@@ -498,11 +506,81 @@ public class SubsetServiceImpl implements SubsetService {
 		target.setRole(source.getRole());
 	}
 
-
 	@Override
 	public List<SubsetCreator> autocompleteCreators(String text) {
 		final HashSet<Long> ids = new HashSet<>(securityUtils.listObjectIdentityIdsForCurrentUser(Subset.class, BasePermission.WRITE));
-		final Predicate predicate = subsetCreator.subset.id.in(ids).and(subsetCreator.fullName.startsWithIgnoreCase(text).or(subsetCreator.institutionalAffiliation.startsWithIgnoreCase(text)));
+		final Predicate predicate = subsetCreator.subset.id.in(ids).and(subsetCreator.fullName.startsWithIgnoreCase(text).or(subsetCreator.institutionalAffiliation
+			.startsWithIgnoreCase(text)));
 		return subsetCreatorRepository.findAll(predicate, new PageRequest(0, 20, new Sort("fullName"))).getContent();
 	}
+
+	@Override
+	@Transactional(readOnly = false)
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	public void rematchSubsetAccessions() {
+		subsetRepository.findAll().forEach(subset -> {
+			rematchSubsetAccessions(subset);
+		});
+	}
+
+	@Override
+	@Transactional(readOnly = false)
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#subset, 'write')")
+	public Subset rematchSubsetAccessions(Subset subset) {
+		subset = subsetRepository.getByUuid(subset.getUuid());
+		LOG.warn("Linking {} accessions with subset {}", subset.getAccessionCount(), subset.getId());
+		subset.setAccessionRefs(lookupMatchingAccessions(subset.getAccessionRefs()));
+		return subsetRepository.save(subset);
+	}
+
+	/**
+	 * Looking for matching Accession and then sets that to AccessionRef
+	 * 
+	 * @param accessionRefs the accessionRefs
+	 *
+	 * @return accessionRefs with matching accessions from Genesys
+	 */
+	private Set<AccessionRef> lookupMatchingAccessions(final Set<AccessionRef> accessionRefs) {
+		List<AccessionRef> list = new ArrayList<>(accessionRefs);
+		List<Accession> foundAccessions = accessionRepository.findById(list);
+
+		LOG.info("Found {} matches for {} identifiers", foundAccessions.size(), accessionRefs.size());
+
+		accessionRefs.forEach(ref -> {
+			Accession foundAccession = foundAccessions.stream().filter(a -> {
+				return StringUtils.equalsIgnoreCase(a.getInstCode(), ref.getInstCode()) && (
+				// when DOI provided
+				(ref.getDoi() != null && a.getDoi() != null && StringUtils.equals(a.getDoi(), ref.getDoi()))
+						// OR when without DOI
+						|| (StringUtils.equalsIgnoreCase(a.getAccessionNumber(), ref.getAcceNumb()) && StringUtils.equalsIgnoreCase(a.getGenus(), ref.getGenus())));
+			}).findFirst().orElse(null);
+			ref.setAccession(foundAccession);
+			if (foundAccession == null) {
+				LOG.debug("No match for {}", ref);
+			}
+		});
+
+		return accessionRefs;
+	}
+
+	@Override
+	@Transactional(readOnly = false, propagation = Propagation.REQUIRED, isolation = Isolation.READ_UNCOMMITTED)
+	public int clearAccessionRefs(Collection<Accession> accessions) {
+		Set<UUID> uuids = accessions.stream().map(a -> a.getUuid()).collect(Collectors.toSet());
+		final Iterable<Subset> datasets = subsetRepository.findAll(QSubset.subset.accessionRefs.any().accession.in(accessions));
+
+		AtomicInteger updates = new AtomicInteger(0);
+		datasets.forEach(subset -> {
+			subset.getAccessionRefs().stream()
+				// filter for matching accessions
+				.filter(ref -> ref.getAccession() != null && uuids.contains(ref.getAccession().getUuid()))
+				// clear accession reference
+				.forEach(ref -> {
+					updates.incrementAndGet();