Finalized migration to updated data model

- Uploader
- JSPs

pom.xml

@@ -645,6 +645,9 @@
 				<artifactId>jetty-maven-plugin</artifactId>
 				<version>${jetty.version}</version>
 				<configuration>
+					<httpConnector>
+						<port>8080</port>
+					</httpConnector>
 					<stopPort>8888</stopPort>
 					<stopKey>stop</stopKey>
 					<jvmArgs>-Dspring.profiles.active=dev -Xmx2048M -Xms1024M -XX:MaxPermSize=128M -Djava.awt.headless=true -server -Dorg.eclipse.jetty.server.Request.maxFormContentSize=5000000</jvmArgs>

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

@@ -36,7 +36,13 @@ import org.springframework.data.elasticsearch.annotations.Document;
 		uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "genus", "acceNumb" }),
 				@UniqueConstraint(name = "UQ_accession_doi", columnNames = { "doi" }) },
 		// Indexes
-		indexes = { @Index(name = "IX_acceNumb", columnList = "acceNumb"), @Index(name = "IX_seqNo", columnList = "seqNo"), @Index(name = "IX_accession_lastModifiedDate", columnList = "lastModifiedDate") })
+		indexes = { 
+				@Index(name = "IX_acceNumb", columnList = "acceNumb"), 
+				@Index(name = "IX_inst_seqNo", columnList = "instituteId,seqNo"), 
+				@Index(name = "IX_origcty_seqNo", columnList = "orgCtyId,seqNo"), 
+				@Index(name = "IX_taxa_seq", columnList = "taxonomyId2,seqNo"), 
+				@Index(name = "IX_seqNo", columnList = "seqNo"), 
+				@Index(name = "IX_accession_lastModifiedDate", columnList = "lastModifiedDate") })
 @Audited
 @Document(indexName = "genesys")
 public class Accession extends AccessionData {

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

@@ -328,7 +328,7 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 
 	@Override
 	public String toString() {
-		return MessageFormat.format("Accession id={0,number,##########} UUID={1}", accessionId.getId(), getUuid());
+		return MessageFormat.format("Accession id={0,number,##########} UUID={1} {2} {3} {4}", accessionId.getId(), getUuid(), instituteCode, accessionNumber, genus);
 	}
 
 	public String getAcceUrl() {
@@ -431,18 +431,35 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 	public Integer getSampleStatus() {
 		return this.sampStat;
 	}
-	
+
 	@Transient
 	@JsonIgnore
 	// For EL
 	public Boolean getAvailable() {
 		return this.available;
 	}
-	
+
+	@Transient
+	@JsonIgnore
+	// For EL
+	public Boolean getAvailability() {
+		return this.available;
+	}
+
 	@Transient
 	@JsonIgnore
 	// For EL
 	public Boolean getHistoric() {
 		return this.historic;
 	}
+	
+
+	@Transient
+	@JsonIgnore
+	// For EL
+	public String getInstCode() {
+		return this.instituteCode;
+	}
+	
+	
 }

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

@@ -114,6 +114,11 @@ public class AccessionId extends AuditedVersionedModel implements IdUUID {
 	@CollectionTable(name = "accession_breedercode", joinColumns = @JoinColumn(name = "accessionId", referencedColumnName = "id"))
 	private Set<String> breederCode;
 
+	@Column(name = "breederName", nullable = false, length = 250)
+	@ElementCollection(fetch = FetchType.LAZY)
+	@CollectionTable(name = "accession_breedername", joinColumns = @JoinColumn(name = "accessionId", referencedColumnName = "id"))
+	private Set<String> breederName;
+
 	@PrePersist
 	private void prepersist() {
 		if (uuid == null) {
@@ -193,6 +198,14 @@ public class AccessionId extends AuditedVersionedModel implements IdUUID {
 	public void setBreederCode(Set<String> breederCode) {
 		this.breederCode = breederCode;
 	}
+	
+	public Set<String> getBreederName() {
+		return breederName;
+	}
+	
+	public void setBreederName(Set<String> breederName) {
+		this.breederName = breederName;
+	}
 
 	public Set<String> getDuplSite() {
 		return duplSite;

src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java

@@ -183,7 +183,7 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	}
 
 	public Long getTaxGenus() {
-		return this.taxGenus;
+		return this.taxGenus == null ? this.getId() : this.taxGenus;
 	}
 
 	public void setTaxGenus(Long taxGenus) {
@@ -191,7 +191,7 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	}
 
 	public Long getTaxSpecies() {
-		return this.taxSpecies;
+		return this.taxSpecies == null ? this.getId() : this.taxSpecies;
 	}
 
 	public void setTaxSpecies(Long taxSpecies) {

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

@@ -97,10 +97,8 @@ public class FaoInstitute extends BasicModel implements GeoReferencedEntity, Acl
 	private Double latitude;
 	private Double longitude;
 	private Double elevation;
-	private boolean uniqueAcceNumbs = true;
-
-	@Column(name = "allowMaterialRequests", columnDefinition = "boolean default true", nullable = false)
-	private boolean allowMaterialRequests = true;
+	private boolean uniqueAcceNumbs = false;
+	private boolean allowMaterialRequests = false;
 
 	public FaoInstitute() {
 	}

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

@@ -162,12 +162,12 @@ public class AccessionRepositoryCustomImpl implements AccessionRepositoryCustom,
 		}
 
 		if (uniqueAcceNumbs) {
-			restrictions.add(root.get("accessionName").in(acceNumbs));
+			restrictions.add(root.get("accessionNumber").in(acceNumbs));
 			LOG.trace("*** {} accenumbs={}", institute.getCode(), acceNumbs);
 		} else {
 			// A lot of .. (acceNumb=? and genus=?)
 			for (AccessionIdentifier3 ah : accessionIds) {
-				restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionName"), ah.getAccessionNumber()), criteriaBuilder.equal(tax.get("genus"), ah.getGenus())));
+				restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionNumber"), ah.getAccessionNumber()), criteriaBuilder.equal(tax.get("genus"), ah.getGenus())));
 			}
 		}
 		cq.where(criteriaBuilder.and(criteriaBuilder.equal(root.get("institute"), institute), criteriaBuilder.or(restrictions.toArray(EMPTY_PREDICATE_ARRAY))));
@@ -206,9 +206,9 @@ public class AccessionRepositoryCustomImpl implements AccessionRepositoryCustom,
 		if (doi != null) {
 			restrictions.add(criteriaBuilder.equal(root.get("doi"), doi));
 		} else if (institute.hasUniqueAcceNumbs()) {
-			restrictions.add(criteriaBuilder.equal(root.get("accessionName"), acceNumb));
+			restrictions.add(criteriaBuilder.equal(root.get("accessionNumber"), acceNumb));
 		} else {
-			restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionName"), acceNumb), criteriaBuilder.equal(tax.get("genus"), genus)));
+			restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionNumber"), acceNumb), criteriaBuilder.equal(tax.get("genus"), genus)));
 		}
 		
 		cq.where(criteriaBuilder.and(criteriaBuilder.equal(root.get("institute"), institute), criteriaBuilder.or(restrictions.toArray(new Predicate[] {}))));

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

@@ -47,6 +47,22 @@ public class DirectMysqlQuery {
 	private static final Logger LOG = LoggerFactory.getLogger(DirectMysqlQuery.class);
 	private static final String SPACE = " ";
 
+	public static final String TABLE_ACCEID = "acce";
+	public static final String TABLE_ACCESSION = "accession";
+	public static final String TABLE_ACCESSION_STORAGE = "accession_storage";
+	public static final String TABLE_ACCESSION_COLLECT = "accession_collect";
+	public static final String TABLE_ACCESSION_ALIAS = "accession_alias";
+	public static final String TABLE_ACCESSION_GEO = "accession_geo";
+	public static final String TABLE_ACCESSION_LIST = "accession_list";
+	public static final String TABLE_ACCESION_LISTITEMS = "accession_listitem";
+	public static final String TABLE_ORGANIZATIONINSTITUTE = "organizationinstitute";
+	public static final String TABLE_CROP = "crop";
+	public static final String TABLE_PDCI = "pdci";
+	public static final String TABLE_TAXONOMY = "taxonomy2";
+	public static final String TABLE_ORGANIZATION = "organization";
+	public static final String TABLE_COUNTRY = "country";
+	public static final String TABLE_FAOINSTITUTE = "faoinstitute";
+
 	final Set<String> tables = new HashSet<String>();
 	final List<Object> params = new ArrayList<Object>();
 	final StringBuffer sb, whereBuffer = new StringBuffer(), sortBuffer = new StringBuffer();
@@ -105,63 +121,65 @@ public class DirectMysqlQuery {
 
 	protected DirectMysqlQuery join(AppliedFilters filters) {
 
+		if (filters.hasFilter(FilterConstants.UUID)) {
+			innerJoin(TABLE_ACCEID, null, "acce.id=a.id");
+		}
+
 		if (filters.hasFilter(FilterConstants.LISTS)) {
-			innerJoin("accelistitems", "ali", "ali.acceid=a.id");
-			innerJoin("accelist", "al", "al.id=ali.listid");
+			innerJoin(TABLE_ACCEID, null, "acce.id=a.id");
+			innerJoin(TABLE_ACCESION_LISTITEMS, "ali", "ali.acceid=acce.id");
+			innerJoin(TABLE_ACCESSION_LIST, "al", "al.id=ali.listid");
 		}
 
-		if (filters.hasFilter(FilterConstants.TAXONOMY_GENUS) || filters.hasFilter(FilterConstants.TAXONOMY_SPECIES)
-				|| filters.hasFilter(FilterConstants.TAXONOMY_SUBTAXA) || filters.hasFilter(FilterConstants.TAXONOMY_SCINAME)) {
+		if (filters.hasFilter(FilterConstants.TAXONOMY_GENUS) || filters.hasFilter(FilterConstants.TAXONOMY_SPECIES) || filters.hasFilter(FilterConstants.TAXONOMY_SUBTAXA)
+				|| filters.hasFilter(FilterConstants.TAXONOMY_SCINAME)) {
 
-			innerJoin("taxonomy2", "t", "t.id=a.taxonomyId2");
+			innerJoin(TABLE_TAXONOMY, "t", "t.id=a.taxonomyId2");
 		}
 
 		if (filters.hasFilter(FilterConstants.CROPS)) {
-			innerJoin("crop", null, "crop.id=a.cropId");
+			innerJoin(TABLE_CROP, null, "crop.id=a.cropId");
 		}
 
-        if (filters.hasFilter(FilterConstants.UUID)) {
-            innerJoin("acce", null, "acce.id=a.id");
-        }
-		
 		if (filters.hasFilter(FilterConstants.PDCI)) {
-			innerJoin("pdci", null, "pdci.accessionId=a.id");
+			innerJoin(TABLE_ACCEID, null, "acce.id=a.id");
+			innerJoin(TABLE_PDCI, null, "pdci.id=acce.pdciId");
 		}
-		
+
 		// if (filters.hasFilter(FilterConstants.ORGCTY_ISO3)) {
 		// innerJoin("country", "cty", "cty.id=a.orgCtyId");
 		// }
 
-		if (/* filters.hasFilter(FilterConstants.INSTCODE) || */filters.hasFilter(FilterConstants.INSTITUTE_COUNTRY_ISO3)
-				|| filters.hasFilter(FilterConstants.INSTITUTE_NETWORK)) {
+		if (filters.hasFilter(FilterConstants.INSTCODE) || filters.hasFilter(FilterConstants.INSTITUTE_COUNTRY_ISO3) || filters.hasFilter(FilterConstants.INSTITUTE_NETWORK)) {
 
-			innerJoin("faoinstitute", "fao", "fao.id=a.instituteId");
+			innerJoin(TABLE_FAOINSTITUTE, "fao", "fao.id=a.instituteId");
 
 			if (filters.hasFilter(FilterConstants.INSTITUTE_COUNTRY_ISO3)) {
-				innerJoin("country", "faocty", "faocty.id=fao.countryId");
+				innerJoin(TABLE_COUNTRY, "faocty", "faocty.id=fao.countryId");
 			}
 
 			if (filters.hasFilter(FilterConstants.INSTITUTE_NETWORK)) {
-				innerJoin("organizationinstitute", "oi", "oi.instituteId=fao.id");
-				innerJoin("organization", "org", "org.id=oi.organizationId");
+				innerJoin(TABLE_ORGANIZATIONINSTITUTE, "oi", "oi.instituteId=fao.id");
+				innerJoin(TABLE_ORGANIZATION, "org", "org.id=oi.organizationId");
 			}
 		}
 
-		if (filters.hasFilter(FilterConstants.GEO_LATITUDE) || filters.hasFilter(FilterConstants.GEO_LONGITUDE)
-				|| filters.hasFilter(FilterConstants.GEO_ELEVATION)) {
-			innerJoin("accessiongeo", "geo", "geo.accessionId=a.id");
+		if (filters.hasFilter(FilterConstants.GEO_LATITUDE) || filters.hasFilter(FilterConstants.GEO_LONGITUDE) || filters.hasFilter(FilterConstants.GEO_ELEVATION)) {
+			innerJoin(TABLE_ACCESSION_GEO, "geo", "geo.id=acce.geoId");
 		}
 
 		if (filters.hasFilter(FilterConstants.ALIAS)) {
-			innerJoin("accessionalias", "accename", "accename.accessionId=a.id");
+			innerJoin(TABLE_ACCESSION_ALIAS, "accename", "accename.accessionId=acce.id");
 		}
 
 		if (filters.hasFilter(FilterConstants.COLLMISSID)) {
-			innerJoin("accessioncollect", "col", "col.accessionId=a.id");
+			innerJoin(TABLE_ACCEID, null, "acce.id=a.id");
+			innerJoin(TABLE_ACCESSION_COLLECT, "col", "col.id=acce.collId");
 		}
 
 		if (filters.hasFilter(FilterConstants.STORAGE)) {
-			outerJoin("accessionstorage", "storage", "storage.accessionId=a.id");
+			innerJoin(TABLE_ACCEID, null, "acce.id=a.id");
+			outerJoin(TABLE_ACCESSION_STORAGE, "storage", "storage.accessionId=acce.id");
 		}
 
 		return this;
@@ -170,17 +188,12 @@ public class DirectMysqlQuery {
 	protected DirectMysqlQuery filter(AppliedFilters filters, MethodResolver methodResolver) {
 		createQuery(whereBuffer, "a.id", filters.get(FilterConstants.ID), params);
 		createQuery(whereBuffer, "acce.uuid", filters.get(FilterConstants.UUID), params);
-		{
-			// FIXME Are these two still used?
-			createQuery(whereBuffer, "t.taxGenus", filters.get("genusId"), params);
-			createQuery(whereBuffer, "t.taxSpecies", filters.get("speciesId"), params);
-		}
 		createQuery(whereBuffer, "al.uuid", filters.get(FilterConstants.LISTS), params);
 		createQuery(whereBuffer, "a.acceNumb", filters.get(FilterConstants.ACCENUMB), params);
 		createQuery(whereBuffer, "a.seqNo", filters.get(FilterConstants.SEQUENTIAL_NUMBER), params);
 		createQuery(whereBuffer, "a.lastModifiedDate", filters.get(FilterConstants.LAST_MODIFIED_DATE), params);
-		createQuery(whereBuffer, "a.orgCty", filters.get(FilterConstants.ORGCTY_ISO3), params);
-		createQuery(whereBuffer, "a.instCode", filters.get(FilterConstants.INSTCODE), params);
+		createQuery(whereBuffer, "a.origCty", filters.get(FilterConstants.ORGCTY_ISO3), params);
+		createQuery(whereBuffer, "fao.code", filters.get(FilterConstants.INSTCODE), params);
 		createQuery(whereBuffer, "a.cropName", filters.get(FilterConstants.CROPNAME), params);
 		createQuery(whereBuffer, "faocty.code3", filters.get(FilterConstants.INSTITUTE_COUNTRY_ISO3), params);
 		createQuery(whereBuffer, "a.inSGSV", filters.get(FilterConstants.SGSV), params);

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

@@ -123,7 +123,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			throw new RuntimeException("Genesys does not support requests for data beyond " + PAGINATION_MAXPAGE_LIMIT + "th page.");
 		}
 
-		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
+		final DirectMysqlQuery directQuery = new DirectMysqlQuery(DirectMysqlQuery.TABLE_ACCESSION, "a");
 		directQuery.jsonFilter(filters, new MethodResolver() {
 			@Override
 			public Method getMethod(long methodId) {
@@ -170,7 +170,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			throw new MaxPageLimitException(PAGINATION_MAXPAGE_LIMIT, pageable.getPageNumber() + 1);
 		}
 
-		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
+		final DirectMysqlQuery directQuery = new DirectMysqlQuery(DirectMysqlQuery.TABLE_ACCESSION, "a");
 		directQuery.jsonFilter(filters, new MethodResolver() {
 			@Override
 			public Method getMethod(long methodId) {
@@ -394,14 +394,16 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			}
 		}
 
-		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accessiongeo", "geo");
-		directQuery.filterTile(zoom, xtile, ytile);
+		final DirectMysqlQuery directQuery = new DirectMysqlQuery(DirectMysqlQuery.TABLE_ACCESSION_GEO, "geo");
 
 		if (!filters.isEmpty() || !distinct) {
 			// Join accession table when we have filters or looking at details
-			directQuery.innerJoin("accession", "a", "a.id=geo.accessionId");
+			directQuery.innerJoin(DirectMysqlQuery.TABLE_ACCEID, null, "acce.geoId=geo.id");
+			directQuery.innerJoin(DirectMysqlQuery.TABLE_ACCESSION, "a", "a.id=acce.id");
 		}
 
+		directQuery.filterTile(zoom, xtile, ytile);
+
 		if (!filters.isEmpty()) {
 			directQuery.join(filters);
 			directQuery.filter(filters, new MethodResolver() {

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

@@ -355,6 +355,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 				accessionId.getAliases().size();
 			if (accessionId.getBreederCode() != null)
 				accessionId.getBreederCode().size();
+			if (accessionId.getBreederName() != null)
+				accessionId.getBreederName().size();
 			if (accessionId.getDuplSite() != null)
 				accessionId.getDuplSite().size();
 			if (accessionId.getRemarks() != null)

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

@@ -208,7 +208,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	public void cleanupTaxonomies() {
 		Set<BigInteger> referencedIds = taxonomy2Repository.findTaxonomyReferencedIds();
 		Set<Long> allIds = taxonomy2Repository.findTaxonomyIds();
-		for (BigInteger integer: referencedIds) {
+		for (BigInteger integer : referencedIds) {
 			allIds.remove(integer.longValue());
 		}
 
@@ -216,13 +216,13 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 			taxonomy2Repository.removeUnusedIds(allIds);
 		}
 	}
-	
 
 	@Override
 	@Transactional(timeout = 50, isolation = Isolation.READ_UNCOMMITTED, propagation = Propagation.REQUIRED)
 	public Taxonomy2 ensureTaxonomy(Taxonomy2 example) {
 		example.sanitize();
-		Taxonomy2 existing = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(example.getGenus(), example.getSpecies(), example.getSpAuthor(), example.getSubtaxa(), example.getSubtAuthor());
+		Taxonomy2 existing = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(example.getGenus(), example.getSpecies(), example.getSpAuthor(), example
+			.getSubtaxa(), example.getSubtAuthor());
 		if (existing == null) {
 			LOG.debug("Adding taxonomy {} {} {} {} {}", example.getGenus(), example.getSpecies(), example.getSpAuthor(), example.getSubtaxa(), example.getSubtAuthor());
 			Taxonomy2 newTaxa = new Taxonomy2();
@@ -231,7 +231,35 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 			newTaxa.setSpAuthor(example.getSpAuthor());
 			newTaxa.setSubtaxa(example.getSubtaxa());
 			newTaxa.setSubtAuthor(example.getSubtAuthor());
-			return taxonomy2Repository.save(newTaxa.sanitize());
+
+			Taxonomy2 tsP = new Taxonomy2();
+			tsP.setGenus(newTaxa.getGenus());
+			tsP.setSpecies(newTaxa.getSpecies());
+			tsP.sanitize();
+			if (tsP.equalTo(newTaxa)) {
+				// equal to species level
+				tsP.setSpecies(null);
+				tsP.sanitize();
+				// get genus id
+				if (!tsP.equalTo(newTaxa)) {
+					tsP = ensureTaxonomy(tsP);
+					newTaxa.setTaxGenus(tsP.getTaxGenus());
+				} else {
+					// incoming taxonomy is genus level only.
+					// System.err.println("What now " + newTaxa + " == " + tsP);
+				}
+			} else {
+				// not equal to species level, ensure taxSpecies
+				tsP = ensureTaxonomy(tsP);
+				newTaxa.setTaxGenus(tsP.getTaxGenus());
+				newTaxa.setTaxSpecies(tsP.getId());
+			}
+
+			Taxonomy2 t = taxonomy2Repository.save(newTaxa.sanitize());
+			// self-references
+			t.setTaxGenus(t.getTaxGenus());
+			t.setTaxSpecies(t.getTaxSpecies());
+			return taxonomy2Repository.save(t);
 		} else {
 			return existing;
 		}

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -18,11 +18,13 @@ package org.genesys2.server.service.worker;
 import java.io.IOException;
 import java.lang.reflect.Field;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.ArrayUtils;
+import org.elasticsearch.common.lang3.StringUtils;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
@@ -112,6 +114,7 @@ public class AccessionUploader implements InitializingBean {
 		assert (updates.isArray());
 		ObjectReader reader = objectMapper.readerFor(Accession.class);
 
+		Date batchDate = new Date();
 		final List<Accession> accessions = new ArrayList<>(updates.size());
 		final List<AccessionOpResponse> responses = new ArrayList<>(updates.size());
 		List<Accession> toSave = new ArrayList<>(updates.size());
@@ -159,12 +162,15 @@ public class AccessionUploader implements InitializingBean {
 			LOG.trace("Upserting: {}", update);
 
 			Accession accession = existingAccessions.stream().filter(existing -> {
-				return (existing.getDoi() != null && existing.getDoi().equals(updateA.getDoi())) || (existing.getInstituteCode().equals(updateA.getInstituteCode()) && existing
-					.getAccessionNumber().equals(updateA.getAccessionNumber()) && existing.getTaxonomy().getGenus().equals(updateA.getTaxonomy().getGenus()));
+				return (existing.getDoi() != null && existing.getDoi().equals(updateA.getDoi()))
+						// or by triplet
+						|| (StringUtils.equalsIgnoreCase(existing.getInstituteCode(), updateA.getInstituteCode()) && StringUtils.equalsIgnoreCase(existing.getAccessionNumber(),
+							updateA.getAccessionNumber()) && StringUtils.equalsIgnoreCase(existing.getTaxonomy().getGenus(), updateA.getTaxonomy().getGenus()));
 			}).findFirst().orElse(null);
 
 			if (accession == null) {
-				LOG.trace("New accesson");
+				// LOG.trace("New accesson");
+				LOG.trace("New accession {} not in {}", update, existingAccessions);
 				response.setResult(new UpsertResult(UpsertResult.Type.INSERT));
 				accession = new Accession();
 				accession.setAccessionId(new AccessionId());
@@ -176,6 +182,7 @@ public class AccessionUploader implements InitializingBean {
 
 			try {
 				accession = applyChanges(update, updateA, accession);
+				accession.setLastModifiedDate(batchDate);
 
 				PDCI pdci = accession.getAccessionId().getPdci();
 				if (pdci == null) {
@@ -215,7 +222,7 @@ public class AccessionUploader implements InitializingBean {
 			if ("taxonomy".equals(fieldName)) {
 				updateTaxonomy(update.get("taxonomy"), updateA.getTaxonomy(), accession);
 
-			} else if ("orgCty".equals(fieldName)) {
+			} else if ("origCty".equals(fieldName)) {
 				updateOrigCty(updateA.getOrigCty(), accession);
 
 			} else if ("geo".equals(fieldName)) {

src/main/java/org/genesys2/server/servlet/controller/AccessionController.java

@@ -34,6 +34,7 @@ import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
@@ -138,34 +139,37 @@ public class AccessionController extends BaseController {
 	 * @return
 	 */
 	public ModelAndView displayAccession(ModelMap model, Accession accession) {
+		AccessionId accessionId = accession.getAccessionId();
+
 		model.addAttribute("accession", accession);
-		model.addAttribute("auditAccession", auditService.auditLogs(accession));
 
-		model.addAttribute("accessionNames", genesysService.listAccessionNames(accession.getAccessionId()));
-		model.addAttribute("accessionAliases", accession.getAccessionId().getAliases());
+		model.addAttribute("accessionNames", genesysService.listAccessionNames(accessionId));
+		model.addAttribute("accessionAliases", accessionId.getAliases());
 		
 		model.addAttribute("accessionExchange", accession);
 		
-		AccessionCollect accessionCollect = accession.getAccessionId().getColl();
+		AccessionCollect accessionCollect = accessionId.getColl();
 		model.addAttribute("accessionCollect", accessionCollect);
 
 		model.addAttribute("accessionBreeding", accession);
 		
-		AccessionGeo accessionGeo = accession.getAccessionId().getGeo();
+		AccessionGeo accessionGeo = accessionId.getGeo();
 		model.addAttribute("accessionGeo", accessionGeo);
 
 		if (SecurityContextHolder.getContext().getAuthentication().isAuthenticated()) {
 			// only for authenticated users
+			model.addAttribute("auditAccession", auditService.auditLogs(accession));
+			model.addAttribute("auditAccessionId", auditService.auditLogs(accessionId));
 			model.addAttribute("auditAccessionCollect", auditService.auditLogs(accessionCollect));
 			model.addAttribute("auditAccessionGeo", auditService.auditLogs(accessionGeo));
 		}
 
-		model.addAttribute("svalbardDeposits", genesysService.getSvalbardData(accession.getAccessionId()));
-		model.addAttribute("accessionRemarks", accession.getAccessionId().getRemarks());
+		model.addAttribute("svalbardDeposits", genesysService.getSvalbardData(accessionId));
+		model.addAttribute("accessionRemarks", accessionId.getRemarks());
 
-		model.addAttribute("metadatas", genesysService.listMetadata(accession.getAccessionId()));
-		model.addAttribute("methods", traitService.listMethods(accession.getAccessionId()));
-		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accession.getAccessionId()));
+		model.addAttribute("metadatas", genesysService.listMetadata(accessionId));
+		model.addAttribute("methods", traitService.listMethods(accessionId));
+		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accessionId));
 
 		if (accession.getCrop() != null) {
 			List<Crop> crops = new ArrayList<Crop>();
@@ -184,7 +188,7 @@ public class AccessionController extends BaseController {
 			}
 		}
 
-		model.addAttribute("pdci", accession.getAccessionId().getPdci());
+		model.addAttribute("pdci", accessionId.getPdci());
 		model.addAttribute("institutePDCI", statisticsService.statisticsPDCI(accession.getInstitute()));
 
 		ImageGallery imageGallery = null;

src/main/java/org/genesys2/server/servlet/controller/RequestController.java

@@ -86,7 +86,7 @@ public class RequestController extends BaseController {
 
 		model.addAttribute("totalCount", selectionBean.size());
 		model.addAttribute("availableCount", genesysService.countAvailableForDistribution(selectionBean.copy()));
-		model.addAttribute("pagedData", genesysService.listAccessions(selectionBean.copy(), new PageRequest(page - 1, 50, new Sort("accessionName"))));
+		model.addAttribute("pagedData", genesysService.listAccessions(selectionBean.copy(), new PageRequest(page - 1, 50, new Sort("accessionNumber"))));
 
 		return "/request/index";
 	}

src/main/java/org/genesys2/server/servlet/controller/SelectionController.java

@@ -87,7 +87,7 @@ public class SelectionController extends BaseController {
 	@RequestMapping(value = "/")
 	public String view(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 
-		model.addAttribute("pagedData", genesysService.listAccessionsDetails(selectionBean.copy(), new PageRequest(page - 1, 50, new Sort("accessionName"))));
+		model.addAttribute("pagedData", genesysService.listAccessionsDetails(selectionBean.copy(), new PageRequest(page - 1, 50, new Sort("accessionNumber"))));
 		model.addAttribute("selection", selectionBean);
 
 		// Add userAccessionLists when authenticated

src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java

@@ -406,6 +406,8 @@ public class AccessionController extends RestController {
 		upgradeRename(update, "acqDate", "acquisitionDate");
 		upgradeRename(update, "bredCode", "breederCode");
 		upgradeRename(update, "mlsStat", "mlsStatus");
+		upgradeRename(update, "orgCty", "origCty");
+
 		
 		if (update.has("geo")) {
 			ObjectNode geo = (ObjectNode) update.get("geo");

src/main/webapp/WEB-INF/jsp/accession/details-turtle.jsp

@@ -29,8 +29,8 @@
   a germplasm:GermplasmAccession;
   germplasm:germplasmID "<c:out value="${accession.id}" />";
   dc:identifier "urn:uuid:<c:out value="${accession.uuid}" />";
-  dwc:catalogNumber "<c:out value="${accession.accessionName}" />";
-  dwc:institutionCode "<c:out value="${accession.instituteCode}" />";
+  dwc:catalogNumber "<c:out value="${accession.accessionNumber}" />";
+  dwc:institutionCode "<c:out value="${accession.institute.code}" />";
   dwc:instituteId "<c:out value="${accession.institute.id}" />";
   dwc:countryCode "<c:out value="${accession.institute.country.code3}" />";
   dwc:genus "<c:out value="${accession.taxonomy.genus}" />";  

src/main/webapp/WEB-INF/jsp/accession/details.jsp

@@ -43,10 +43,10 @@
 </p> --%>
 
     <%--
-		<gui:alert type="warning" display="${accession.availability eq false}">
+		<gui:alert type="warning" display="${accession.available eq false}">
 			<spring:message code="accession.not-available-for-distribution" />
 		</gui:alert>
-		<gui:alert type="info" display="${accession.availability eq true}">
+		<gui:alert type="info" display="${accession.available eq true}">
 			<spring:message code="accession.available-for-distribution" />
 		</gui:alert>
 	--%>
@@ -244,6 +244,7 @@
             </div>
           </div>