PDCI included in ES, aspects pick up recalculations

src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java

@@ -89,6 +89,7 @@ public class AccessionDetails {
 
 	private Date modifiedDate;
 	private Date acqusitionDate;
+	private Float pdciScore;
 
 	private boolean historic;
 
@@ -122,7 +123,12 @@ public class AccessionDetails {
 		ad.sampStat = accession.getSampleStatus();
 		ad.storage = new ArrayList<Integer>(accession.getStoRage());
 		ad.lists = new HashSet<String>();
-		ad.cropName=accession.getCropName();
+		ad.cropName = accession.getCropName();
+
+		if (accession.getAccessionId().getPdci() != null) {
+			ad.pdciScore = accession.getAccessionId().getPdci().getScore();
+		}
+
 		for (AccessionList al : accession.getAccessionId().getLists()) {
 			ad.lists.add(al.getUuid().toString());
 		}
@@ -501,4 +507,11 @@ public class AccessionDetails {
 		this.lists = lists;
 	}
 
+	public void setPdciScore(Float pdciScore) {
+		this.pdciScore = pdciScore;
+	}
+
+	public Float getPdciScore() {
+		return pdciScore;
+	}
 }

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

@@ -29,6 +29,7 @@ import javax.persistence.JoinColumn;
 import javax.persistence.JoinTable;
 import javax.persistence.ManyToMany;
 import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
 import javax.persistence.PrePersist;
 import javax.persistence.Table;
 
@@ -37,8 +38,7 @@ import org.genesys2.server.model.VersionedAuditedModel;
 import org.genesys2.server.model.impl.AccessionList;
 
 /**
- * Entity holds the assigned accession identifiers regardless of active or
- * historic records.
+ * Entity holds the assigned accession identifiers regardless of active or historic records.
  */
 @Entity
 @Inheritance(strategy = InheritanceType.JOINED)
@@ -60,6 +60,9 @@ public class AccessionId extends VersionedAuditedModel implements IdUUID {
 	@JoinTable(name = "accelistitems", joinColumns = @JoinColumn(name = "acceid"), inverseJoinColumns = @JoinColumn(name = "listid"))
 	private Set<AccessionList> lists;
 
+	@OneToOne(mappedBy = "accession", fetch = FetchType.LAZY, optional = true, orphanRemoval = true)
+	private PDCI pdci;
+
 	@PrePersist
 	private void prepersist() {
 		if (uuid == null) {
@@ -83,6 +86,11 @@ public class AccessionId extends VersionedAuditedModel implements IdUUID {
 	public void setLists(Set<AccessionList> lists) {
 		this.lists = lists;
 	}
+
+	public PDCI getPdci() {
+		return pdci;
+	}
+
 	//
 	// public List<AccessionTrait> getTraits() {
 	// return traits;

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

@@ -21,6 +21,7 @@ import java.util.Set;
 
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
+import javax.persistence.Index;
 import javax.persistence.JoinColumn;
 import javax.persistence.OneToOne;
 import javax.persistence.PrePersist;
@@ -31,14 +32,14 @@ import javax.persistence.Transient;
 import org.genesys2.server.model.VersionedModel;
 
 @Entity
-@Table(name = "pdci")
-public class PDCI extends VersionedModel {
+@Table(name = "pdci", indexes = { @Index(columnList = "score") })
+public class PDCI extends VersionedModel implements AccessionRelated {
 	private static final long serialVersionUID = -1312366054528702261L;
 
-	public static final String[] independentItems = { "genus", "species", "spAuthor", "subTaxa", "subtAuthor", "cropName", "acqDate", "sampStat", "donorCode",
-			"donorNumb", "otherNumb", "duplSite", "storage", "donorName", "duplInstName", "acceUrl", "mlsStat" };
-	public static final String[] dependentItems = { "origCty", "collSite", "latitude", "longitude", "elevation", "collDate", "bredCode", "ancest", "collSrc",
-			"acceName", "collNumb", "collCode", "collName" };
+	public static final String[] independentItems = { "genus", "species", "spAuthor", "subTaxa", "subtAuthor", "cropName", "acqDate", "sampStat", "donorCode", "donorNumb", "otherNumb", "duplSite",
+			"storage", "donorName", "duplInstName", "acceUrl", "mlsStat" };
+	public static final String[] dependentItems = { "origCty", "collSite", "latitude", "longitude", "elevation", "collDate", "bredCode", "ancest", "collSrc", "acceName", "collNumb", "collCode",
+			"collName" };
 
 	@OneToOne(cascade = {}, fetch = FetchType.LAZY, optional = false)
 	@JoinColumn(name = "accessionId")
@@ -86,6 +87,7 @@ public class PDCI extends VersionedModel {
 		this.scoreHist = (float) (Math.ceil(this.score * 2) / 2);
 	}
 
+	@Override
 	public AccessionId getAccession() {
 		return accession;
 	}

src/main/java/org/genesys2/server/persistence/domain/AccessionIdRepository.java

@@ -16,6 +16,7 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.util.Collection;
 import java.util.List;
 
 import org.genesys2.server.model.genesys.AccessionId;
@@ -28,7 +29,10 @@ public interface AccessionIdRepository extends JpaRepository<AccessionId, Long>
 	@Query("select aid from AccessionId aid where aid.uuid is null")
 	List<AccessionId> findMissingUuid(Pageable pageable);
 
-	@Query("select aid from AccessionId aid, PDCI pdci where pdci.accession=aid and pdci.score is null")
+	@Query("select aid from AccessionId aid left join aid.pdci pdci where pdci.score is null")
 	List<AccessionId> findMissingPDCI(Pageable pageable);
 
+	@Query("select aid from AccessionId aid left join aid.pdci pdci where pdci.score is null")
+	Collection<AccessionId> findMissingPDCI();
+
 }

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

@@ -81,4 +81,6 @@ public interface FilterConstants {
 
 	public static final String LISTS = "lists";
 
+	public static final String PDCI = "pdci";
+
 }

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

@@ -18,7 +18,6 @@ package org.genesys2.server.service;
 
 import java.io.IOException;
 import java.io.OutputStream;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
@@ -261,7 +260,7 @@ public interface GenesysService {
 
 	List<PDCI> loadPDCI(List<Long> batch);
 
-	int generateMissingPDCI(int count);
+	List<PDCI> updatePDCI(Set<Long> ids);
 
 	PDCIStatistics statisticsPDCI(Organization organization);
 
@@ -269,6 +268,6 @@ public interface GenesysService {
 
 	void regenerateAccessionSequentialNumber();
 
-	List<Accession> saveAccessionCrops(ArrayList<Long> accessionIds);
+	List<Accession> saveAccessionCrops(List<Long> accessionIds);
 
 }

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

@@ -120,6 +120,10 @@ public class DirectMysqlQuery {
 			innerJoin("crop", null, "crop.id=a.cropId");
 		}
 		
+		if (filters.hasFilter(FilterConstants.PDCI)) {
+			innerJoin("pdci", null, "pdci.accessionId=a.id");
+		}
+		
 		// if (filters.hasFilter(FilterConstants.ORGCTY_ISO3)) {
 		// innerJoin("country", "cty", "cty.id=a.orgCtyId");
 		// }
@@ -201,6 +205,7 @@ public class DirectMysqlQuery {
 		createQuery(whereBuffer, "accename.name", filters.get(FilterConstants.ALIAS), params);
 		createQuery(whereBuffer, "col.collMissId", filters.get(FilterConstants.COLLMISSID), params);
 		createQuery(whereBuffer, "storage.storage", filters.get(FilterConstants.STORAGE), params);
+		createQuery(whereBuffer, "pdci.score", filters.get(FilterConstants.PDCI), params);
 
 		for (final AppliedFilter methodFilter : filters.methodFilters()) {
 			// Handle Genesys Method!

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

@@ -77,8 +77,7 @@ public class FilterHandler {
 	private final ArrayList<GenesysFilter> availableFilters;
 
 	/**
-	 * By default we exclude historic records unless the user explicitly
-	 * specifies otherwise.
+	 * By default we exclude historic records unless the user explicitly specifies otherwise.
 	 */
 	public static final AppliedFilter NON_HISTORIC_FILTER = new AppliedFilter().setFilterName(FilterConstants.HISTORIC).addFilterValue(new LiteralValueFilter(false));
 
@@ -89,8 +88,8 @@ public class FilterHandler {
 		this.availableFilters.add(new BasicFilter(FilterConstants.CROPNAME, DataType.STRING));
 		this.availableFilters.add(new BasicFilter(FilterConstants.LISTS, DataType.STRING));
 
-		this.availableFilters.add(new I18nListFilter<Integer>(FilterConstants.SAMPSTAT, DataType.NUMERIC).build("accession.sampleStatus", new Integer[] { 100,
-				110, 120, 130, 200, 300, 400, 410, 411, 412, 413, 414, 415, 416, 420, 421, 422, 423, 500, 600, 999 }));
+		this.availableFilters.add(new I18nListFilter<Integer>(FilterConstants.SAMPSTAT, DataType.NUMERIC).build("accession.sampleStatus",
+				new Integer[] { 100, 110, 120, 130, 200, 300, 400, 410, 411, 412, 413, 414, 415, 416, 420, 421, 422, 423, 500, 600, 999 }));
 		this.availableFilters.add(new AutocompleteFilter(FilterConstants.TAXONOMY_GENUS, "/explore/ac/" + FilterConstants.TAXONOMY_GENUS));
 		this.availableFilters.add(new AutocompleteFilter(FilterConstants.TAXONOMY_SPECIES, "/explore/ac/" + FilterConstants.TAXONOMY_SPECIES));
 		this.availableFilters.add(new AutocompleteFilter(FilterConstants.TAXONOMY_SUBTAXA, "/explore/ac/" + FilterConstants.TAXONOMY_SUBTAXA));
@@ -113,8 +112,8 @@ public class FilterHandler {
 		this.availableFilters.add(new BasicFilter(FilterConstants.AVAILABLE, DataType.BOOLEAN));
 		this.availableFilters.add(new BasicFilter(FilterConstants.HISTORIC, DataType.BOOLEAN).allowsNull(false));
 		this.availableFilters.add(new BasicFilter(FilterConstants.COLLMISSID, DataType.STRING).setAnalyzed(true));
-		this.availableFilters.add(new I18nListFilter<Integer>(FilterConstants.STORAGE, DataType.NUMERIC).build("accession.storage", new Integer[] { 10, 11, 12,
-				13, 20, 30, 40, 50, 99 }));
+		this.availableFilters.add(new I18nListFilter<Integer>(FilterConstants.STORAGE, DataType.NUMERIC).build("accession.storage", new Integer[] { 10, 11, 12, 13, 20, 30, 40, 50, 99 }));
+		this.availableFilters.add(new BasicFilter(FilterConstants.PDCI, DataType.NUMERIC).allowsNull(false));
 	}
 
 	public List<GenesysFilter> listAvailableFilters() {
@@ -378,8 +377,7 @@ public class FilterHandler {
 		}
 
 		/**
-		 * Returns true if the filter is listed and has at least one value
-		 * specified
+		 * Returns true if the filter is listed and has at least one value specified
 		 * 
 		 * @param filterName
 		 * @return
@@ -751,7 +749,7 @@ public class FilterHandler {
 		public String toString() {
 			return getClass().getSimpleName() + " " + getType() + ": " + getTo();
 		}
-		
+
 		@Override
 		public int hashCode() {
 			final int prime = 31;
@@ -809,13 +807,11 @@ public class FilterHandler {
 			return from;
 		}
 
-
 		@Override
 		public String toString() {
 			return getClass().getSimpleName() + " " + getType() + ": " + getFrom();
 		}
-		
-		
+
 		@Override
 		public int hashCode() {
 			final int prime = 31;
@@ -873,7 +869,7 @@ public class FilterHandler {
 		public String toString() {
 			return getClass().getSimpleName() + " startsWith " + getStartsWith();
 		}
-				
+
 		@Override
 		public int hashCode() {
 			final int prime = 31;

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

@@ -32,6 +32,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.UUID;
+import java.util.stream.Collectors;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
@@ -287,8 +288,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			} else {
 
 				try {
-					Accession accnByAlias = accessionAliasRepository.findAccession(aid3.getHoldingInstitute(), aid3.getAccessionName(),
-							AccessionAlias.AliasType.OTHERNUMB.getId());
+					Accession accnByAlias = accessionAliasRepository.findAccession(aid3.getHoldingInstitute(), aid3.getAccessionName(), AccessionAlias.AliasType.OTHERNUMB.getId());
 
 					if (accnByAlias != null) {
 						LOG.info("Found accession by alias " + accnByAlias);
@@ -506,71 +506,83 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 
 	@Override
 	public List<AllStuff> loadAllStuff(Collection<Long> accessionIds) {
-		List<AllStuff> alls = new ArrayList<AllStuff>(accessionIds.size());
 		if (accessionIds == null || accessionIds.size() == 0) {
-			return alls;
+			return Collections.emptyList();
 		}
-		HashMap<Long, AllStuff> map = new HashMap<Long, AllStuff>();
 
-		for (Long accessionId : accessionIds) {
-			AllStuff all = new AllStuff(accessionId);
-			alls.add(all);
-			map.put(accessionId, all);
-		}
-		for (AccessionData a : accessionRepository.findAll(accessionIds)) {
+		final Map<Long, AllStuff> map = Collections.synchronizedMap(new HashMap<Long, AllStuff>());
+
+		List<AllStuff> alls = accessionIds.stream().map(accessionId -> new AllStuff(accessionId)).peek(all -> map.put(all.id, all)).collect(Collectors.toList());
+
+		accessionRepository.findAll(accessionIds).stream().forEach(a -> {
 			AllStuff all = map.get(a.getAccessionId().getId());
 			all.accession = a;
-			a.getAccessionId().getLists().size();
-			// Don't use a#getStorage()
-			a.getStoRage().size();
-			all.names = new ArrayList<AccessionAlias>();
-			all.remarks = new ArrayList<AccessionRemark>();
-		}
+			if (a.getAccessionId().getLists() != null)
+				a.getAccessionId().getLists().size();
+			if (a.getStoRage() != null)
+				// Lazy load stoRage
+				a.getStoRage().size();
+			all.names = new ArrayList<>();
+			all.remarks = new ArrayList<>();
+		});
+
+		accessionHistoricRepository.findAll(accessionIds).stream().forEach(a -> {
+			AllStuff all = map.get(a.getAccessionId().getId());
+			all.accession = a;
+			if (a.getAccessionId().getLists() != null)
+				// Lazy load lists
+				a.getAccessionId().getLists().size();
+			if (a.getStoRage() != null)
+				// Lazy load stoRage
+				a.getStoRage().size();
+			all.names = new ArrayList<>();
+			all.remarks = new ArrayList<>();
+		});
 
-		for (AccessionCollect c : accessionCollectRepository.findAllFor(accessionIds)) {
+		accessionCollectRepository.findAllFor(accessionIds).stream().forEach(c -> {
 			AllStuff all = map.get(c.getAccession().getId());
 			all.collect = c;
-		}
+		});
 
-		for (AccessionGeo g : accessionGeoRepository.findAllFor(accessionIds)) {
+		accessionGeoRepository.findAllFor(accessionIds).stream().forEach(g -> {
 			AllStuff all = map.get(g.getAccession().getId());
 			all.geo = g;
-		}
+		});
 
-		for (AccessionBreeding b : accessionBreedingRepository.findAllFor(accessionIds)) {
+		accessionBreedingRepository.findAllFor(accessionIds).stream().forEach(b -> {
 			AllStuff all = map.get(b.getAccession().getId());
 			all.bred = b;
-		}
+		});
 
-		for (AccessionExchange e : accessionExchangeRepository.findAllFor(accessionIds)) {
+		accessionExchangeRepository.findAllFor(accessionIds).stream().forEach(e -> {
 			AllStuff all = map.get(e.getAccession().getId());
 			all.exch = e;
-		}
+		});
 
-		for (SvalbardData e : svalbardRepository.findAllFor(accessionIds)) {
-			AllStuff all = map.get(e.getId());
-			all.svalbard = e;
-		}
+		svalbardRepository.findAllFor(accessionIds).stream().forEach(sd -> {
+			AllStuff all = map.get(sd.getId());
+			all.svalbard = sd;
+		});
 
-		for (AccessionAlias aa : accessionAliasRepository.findAllFor(accessionIds)) {
+		accessionAliasRepository.findAllFor(accessionIds).stream().forEach(aa -> {
 			if (aa == null) {
-				System.err.println("aa is null");
-				continue;
+				LOG.warn("aa is null");
+				return;
 			}
 			AllStuff all = map.get(aa.getAccession().getId());
 			if (all == null) {
-				System.err.println(aa.getAccession().getId() + " not in the list! " + aa);
+				LOG.warn(aa.getAccession().getId() + " not in the list! " + aa);
 			} else {
 				all.names.add(aa);
 			}
-		}
+		});
 
-		for (AccessionRemark ar : accessionRemarkRepository.findAllFor(accessionIds)) {
+		accessionRemarkRepository.findAllFor(accessionIds).stream().forEach(ar -> {
 			AllStuff all = map.get(ar.getAccession().getId());
 			all.remarks.add(ar);
-		}
+		});
 
-		for (AllStuff all : alls) {
+		alls.stream().forEach(all -> {
 			detach(all.accession);
 			detach(all.geo);
 			detach(all.collect);
@@ -578,7 +590,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			detach(all.names);
 			detach(all.exch);
 			detach(all.remarks);
-		}
+		});
 
 		return alls;
 	}
@@ -674,7 +686,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public Page<Object[]> statisticsCropNameByInstitute(FaoInstitute institute, Pageable pageable) {
 		return accessionRepository.statisticsCropNameInInstitute(institute, pageable);
 	}
-	
+
 	@Override
 	public Page<Object[]> statisticsGenusByInstitute(FaoInstitute institute, Pageable pageable) {
 		return accessionRepository.statisticsGenusInInstitute(institute, pageable);
@@ -796,7 +808,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public List<Accession> saveAccessions(Iterable<Accession> accessions) {
 		Set<FaoInstitute> institutes = new HashSet<FaoInstitute>();
 		for (Accession accession : accessions) {
-//			System.out.println("Saving " + accession + " STO=" + accession.getStoRage() + " ST=" + accession.getStorage());
+			// System.out.println("Saving " + accession + " STO=" + accession.getStoRage() + " ST=" +
+			// accession.getStorage());
 			institutes.add(accession.getInstitute());
 		}
 		List<Accession> res = accessionRepository.save(accessions);
@@ -1214,8 +1227,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	private void writeAccessionsCore(final AppliedFilters filters, ZipOutputStream zos) throws IOException {
 		@SuppressWarnings("resource")
 		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
-		csv.writeNext(new String[] { "genesysId", "uuid", "instCode", "acceNumb", "genus", "species", "fullTaxa", "orgCty", "acqSrc", "acqDate", "mlsStat",
-				"available", "historic", "storage", "sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
+		csv.writeNext(new String[] { "genesysId", "uuid", "instCode", "acceNumb", "genus", "species", "fullTaxa", "orgCty", "acqSrc", "acqDate", "mlsStat", "available", "historic", "storage",
+				"sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
 
 		final ResultSetHelper csvResultsetHelper = new CSVResultSetHelper();
 
@@ -1305,8 +1318,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	private void writeAccessionsColl(final AppliedFilters filters, ZipOutputStream zos) throws IOException {
 		@SuppressWarnings("resource")
 		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
-		csv.writeNext(new String[] { "genesysId", "collMissId", "collNumb", "collDate", "collSrc", "collSite", "collCode", "collName", "collInstAddress",
-				"version" });
+		csv.writeNext(new String[] { "genesysId", "collMissId", "collNumb", "collDate", "collSrc", "collSite", "collCode", "collName", "collInstAddress", "version" });
 
 		final ResultSetHelper csvResultsetHelper = new ResultSetHelperService();
 
@@ -1399,8 +1411,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		for (int i = 0; i < metadataMethods.size(); i++) {
 			final Method method = metadataMethods.get(i);
 
-			osw.write(
-					"<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
+			osw.write("<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 			osw.write("\t<files><location>");
 			osw.write(method.getFieldName().toLowerCase());
 			osw.write(".csv</location></files>\n");
@@ -1632,31 +1643,23 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Override
 	@Transactional
 	@CacheEvict(value = "statistics", allEntries = true)
-	public int generateMissingPDCI(int count) {
-		List<AccessionId> accessionIds = accessionIdRepository.findMissingPDCI(new PageRequest(0, count));
-		Set<Long> ids = new HashSet<Long>();
-		for (AccessionId id : accessionIds) {
-			if (id != null) {
-				ids.add(id.getId());
-			}
-		}
-		Collection<AccessionDetails> ads = getAccessionDetails(ids);
-		List<PDCI> pdcis = new ArrayList<PDCI>();
-		for (AccessionDetails ad : ads) {
-			PDCI pdci = new PDCI();
-			AccessionId accessionId = null;
-			for (AccessionId id : accessionIds) {
-				if (id.getId().equals(ad.getId())) {
-					accessionId = id;
-				}
+	public List<PDCI> updatePDCI(final Set<Long> ids) {
+		LOG.info("Calculating PDCI for " + ids.size() + " accessions");
+		final List<PDCI> pdcis = Collections.synchronizedList(new ArrayList<PDCI>(ids.size()));
+
+		getAccessionDetails(ids).stream().forEach(ad -> {
+			PDCI pdci = repoPdci.findByAccessionId(ad.getId());
+			if (pdci == null) {
+				pdci = new PDCI();
+				pdci.setAccession(accessionIdRepository.findOne(ad.getId()));
 			}
-			pdci.setAccession(accessionId);
 			pdciCalculator.updatePdci(pdci, ad);
 			pdcis.add(pdci);
-		}
-		LOG.info("Generated " + accessionIds.size() + " new PDCIs");
+		});
+
+		LOG.info("Generated " + pdcis.size() + " new PDCIs");
 		repoPdci.save(pdcis);
-		return pdcis.size();
+		return pdcis;
 	}
 
 	@Override
@@ -1794,11 +1797,10 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		genesysLowlevelRepository.updateAccessionSequentialNumber(batch);
 	}
 
-	
 	@Override
 	@Transactional(readOnly = false, propagation = Propagation.REQUIRES_NEW)
 	// @PreAuthorize("hasRole('ADMINISTRATOR')")
-	public List<Accession> saveAccessionCrops(ArrayList<Long> accessionIds) {
+	public List<Accession> saveAccessionCrops(List<Long> accessionIds) {
 		List<Accession> accessions = new ArrayList<>(accessionRepository.findAll(accessionIds));
 		for (Accession accession : accessions) {
 			accessionRepository.updateCrop(accession, cropService.getCrop(accession.getCropName()));

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

@@ -16,12 +16,27 @@
 
 package org.genesys2.server.service.impl;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.genesys2.server.model.genesys.*;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.Metadata;
+import org.genesys2.server.model.genesys.Method;
+import org.genesys2.server.model.genesys.Parameter;
+import org.genesys2.server.model.genesys.ParameterCategory;
 import org.genesys2.server.model.impl.Crop;
-import org.genesys2.server.persistence.domain.*;
+import org.genesys2.server.persistence.domain.AccessionTraitRepository;
+import org.genesys2.server.persistence.domain.GenesysLowlevelRepository;
+import org.genesys2.server.persistence.domain.MetadataMethodRepository;
+import org.genesys2.server.persistence.domain.MethodRepository;
+import org.genesys2.server.persistence.domain.ParameterCategoryRepository;
+import org.genesys2.server.persistence.domain.ParameterRepository;
+import org.genesys2.server.persistence.domain.TraitValueRepository;
 import org.genesys2.server.security.AuthUserDetails;
 import org.genesys2.server.service.AclService;
 import org.genesys2.server.service.HtmlSanitizer;
@@ -39,18 +54,13 @@ import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
 @Service
 @Transactional(readOnly = true)
 public class TraitServiceImpl implements TraitService {
 	public static final Log LOG = LogFactory.getLog(GenesysServiceImpl.class);
 
 	@Autowired
-    @Qualifier("genesysLowlevelRepositoryCustomImpl")
+	@Qualifier("genesysLowlevelRepositoryCustomImpl")
 	private GenesysLowlevelRepository genesysLowlevelRepository;
 	@Autowired
 	private AclService aclService;
@@ -68,8 +78,6 @@ public class TraitServiceImpl implements TraitService {
 	@Autowired
 	private AccessionTraitRepository accessionTraitRepository;
 	@Autowired
-	private MetadataRepository metadataRepository;
-	@Autowired
 	private MetadataMethodRepository metadataMethodRepository;
 
 	@Override
@@ -205,8 +213,7 @@ public class TraitServiceImpl implements TraitService {
 	@Override
 	@PreAuthorize("isAuthenticated()")
 	@Transactional(readOnly = false)
-	public Method addMethod(String rdfUri, String description, String i18n, String unit, String fieldName, int fieldType, Integer fieldSize, String options,