Support for DOI upload

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

@@ -17,13 +17,15 @@
 package org.genesys2.server.persistence.domain;
 
 import java.util.List;
+import java.util.Set;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
+import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 
 public interface AccessionCustomRepository {
 
-	List<Accession> find(FaoInstitute institute, List<String> acceNumbs, List<String> genera) throws NonUniqueAccessionException;
+	List<Accession> find(FaoInstitute institute, Set<AccessionHeaderJson> accessionIds) throws NonUniqueAccessionException;
 
 }

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

@@ -20,6 +20,7 @@ import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
@@ -30,12 +31,13 @@ import javax.persistence.criteria.JoinType;
 import javax.persistence.criteria.Predicate;
 import javax.persistence.criteria.Root;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
+import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.stereotype.Repository;
 import org.springframework.transaction.annotation.Transactional;
@@ -43,7 +45,7 @@ import org.springframework.transaction.annotation.Transactional;
 @Repository
 @Transactional(readOnly = true)
 public class AccessionCustomRepositoryImpl implements AccessionCustomRepository, InitializingBean {
-	public static final Log LOG = LogFactory.getLog(AccessionCustomRepositoryImpl.class);
+	public static final Logger LOG = LoggerFactory.getLogger(AccessionCustomRepositoryImpl.class);
 
 	@PersistenceContext
 	private EntityManager em;
@@ -51,11 +53,12 @@ public class AccessionCustomRepositoryImpl implements AccessionCustomRepository,
 	private CriteriaBuilder criteriaBuilder;
 
 	@Override
-	public List<Accession> find(FaoInstitute institute, List<String> acceNumbs, List<String> genera) throws NonUniqueAccessionException {
+	public List<Accession> find(FaoInstitute institute, Set<AccessionHeaderJson> accessionIds) throws NonUniqueAccessionException {
 		boolean uniqueAcceNumbs = institute.hasUniqueAcceNumbs();
 
 		CriteriaQuery<Accession> cq = criteriaBuilder.createQuery(Accession.class);
 		Root<Accession> root = cq.from(Accession.class);
+		cq.distinct(true);
 		cq.select(root);
 		root.fetch("stoRage", JoinType.LEFT);
 
@@ -65,19 +68,26 @@ public class AccessionCustomRepositoryImpl implements AccessionCustomRepository,
 		}
 		List<Predicate> restrictions = new ArrayList<Predicate>();
 
+		Set<String> uniqueDois = accessionIds.stream().map(aid -> aid.doi).filter(doi -> doi != null).distinct().collect(Collectors.toSet());
+		Set<String> acceNumbs = accessionIds.stream().map(aid -> aid.acceNumb).filter(acceNumb -> acceNumb != null).distinct().collect(Collectors.toSet());
+
+		if (uniqueDois.size() > 0) {
+			restrictions.add(root.get("doi").in(uniqueDois));
+			LOG.debug("*** {} dois={}", institute.getCode(), uniqueDois);
+		}
+
 		if (uniqueAcceNumbs) {
 			restrictions.add(root.get("accessionName").in(acceNumbs));
 			if (LOG.isDebugEnabled())
-				LOG.debug("*** " + institute.getCode() + " " + acceNumbs);
+				LOG.debug("*** {} accenumbs={}", institute.getCode(), acceNumbs);
 		} else {
 			// A lot of .. (acceNumb=? and genus=?)
-			for (int i = 0; i < acceNumbs.size(); i++) {
-				restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionName"), acceNumbs.get(i)),
-						criteriaBuilder.equal(tax.get("genus"), genera.get(i))));
+			for (AccessionHeaderJson ah : accessionIds) {
+				restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionName"), ah.acceNumb), criteriaBuilder.equal(tax.get("genus"), ah.genus)));
 			}
 		}
 		cq.where(criteriaBuilder.and(criteriaBuilder.equal(root.get("institute"), institute), criteriaBuilder.or(restrictions.toArray(new Predicate[] {}))));
-		cq.distinct(true);
+
 		List<Accession> res = em.createQuery(cq).getResultList();
 
 		if (LOG.isDebugEnabled())

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

@@ -16,7 +16,7 @@
 
 package org.genesys2.server.service.impl;
 
-import static org.genesys2.util.NumberUtils.*;
+import static org.genesys2.util.NumberUtils.areEqual;
 
 import java.util.ArrayList;
 import java.util.Date;
@@ -26,6 +26,10 @@ import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
 import org.apache.commons.lang.StringUtils;
@@ -60,15 +64,12 @@ import org.genesys2.server.servlet.controller.rest.PleaseRetryException;
 import org.genesys2.server.servlet.controller.rest.model.AccessionAliasJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
+import org.genesys2.util.DOIUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 @Service
 public class BatchRESTServiceImpl implements BatchRESTService {
 
@@ -97,7 +98,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 	@Autowired
 	private TaxonomyManager taxonomyManager;
-	
+
 	@Override
 	// Read-only, everything happens in manager
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
@@ -131,21 +132,17 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 			Taxonomy2 ensuredTaxonomy = null;
 			try {
-				ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-						current.getSubtAuthor());
+				ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(), current.getSubtAuthor());
 			} catch (Throwable e) {
-				LOG.warn("*** lower(t.genus)=lower(" + current.getGenus() + ") and lower(t.species)=lower(" + current.getSpecies()
-						+ ") and lower(t.spauthor)=lower(" + current.getSpAuthor() + ") and lower(t.subtaxa)=lower(" + current.getSubtaxa()
-						+ ") and lower(subtauthor)=lower(" + current.getSubtAuthor() + ")");
+				LOG.warn("*** lower(t.genus)=lower(" + current.getGenus() + ") and lower(t.species)=lower(" + current.getSpecies() + ") and lower(t.spauthor)=lower(" + current
+					.getSpAuthor() + ") and lower(t.subtaxa)=lower(" + current.getSubtaxa() + ") and lower(subtauthor)=lower(" + current.getSubtAuthor() + ")");
 			}
 			if (ensuredTaxonomy == null) {
 				LOG.warn("Adding new taxonomy: " + current);
-				ensuredTaxonomy = taxonomyManager.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-						current.getSubtAuthor());
+				ensuredTaxonomy = taxonomyManager.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(), current.getSubtAuthor());
 				LOG.info("Registered: " + ensuredTaxonomy);
 
-				ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-						current.getSubtAuthor());
+				ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(), current.getSubtAuthor());
 
 				if (ensuredTaxonomy == null) {
 					throw new PleaseRetryException("Something is wrong with taxonomyManager for " + current.toString());
@@ -197,17 +194,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		final Map<AccessionId, ArrayNode> donorNumbs = new HashMap<AccessionId, ArrayNode>();
 		final Map<AccessionId, ArrayNode> collNumbs = new HashMap<AccessionId, ArrayNode>();
 
-		List<String> acceNumbs = new ArrayList<String>();
-		List<String> genera = new ArrayList<String>();
-		for (AccessionHeaderJson dataJson : batch.keySet()) {
-			acceNumbs.add(dataJson.acceNumb);
-			genera.add(dataJson.genus);
-		}
-
 		List<Accession> loaded = null;
 
 		try {
-			loaded = accessionCustomRepository.find(institute, acceNumbs, genera);
+			loaded = accessionCustomRepository.find(institute, batch.keySet());
 		} catch (NonUniqueAccessionException e) {
 			LOG.warn(e.getMessage());
 			throw new RESTApiException(e.getMessage());
@@ -226,10 +216,18 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				throw new RESTApiException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
 			}
 
-			Accession accession = loaded.stream()
-					.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb))
-							: (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus)))
-					.findFirst().orElse(null);
+			Accession accession = loaded.stream().filter(a -> {
+				if (StringUtils.isNotBlank(a.getDoi())) {
+					if (a.getDoi().equals(dataJson.doi))
+						return true;
+				}
+
+				if (useUniqueAcceNumbs) {
+					return a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb);
+				} else {
+					return a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus);
+				}
+			}).findFirst().orElse(null);
 
 			final ObjectNode accnJson = batch.get(dataJson);
 
@@ -241,6 +239,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				accession.setAccessionId(new AccessionId());
 
 				accession.setInstitute(institute);
+				accession.setDoi(dataJson.doi);
 				accession.setAccessionName(dataJson.acceNumb);
 
 				if (accnJson.get(Api1Constants.Accession.GENUS) == null && accnJson.get(Api1Constants.Accession.GENUS_NEW) == null) {
@@ -257,14 +256,18 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				upsertResult.setUUID(accession.getUuid());
 			}
 
-			if (accession.getAccessionId().isPersisted() || useUniqueAcceNumbs && accnJson.get(Api1Constants.Accession.GENUS) != null
-					|| accnJson.get(Api1Constants.Accession.GENUS_NEW) != null || accnJson.get(Api1Constants.Accession.SPECIES) != null
-					|| accnJson.get(Api1Constants.Accession.SPAUTHOR) != null || accnJson.get(Api1Constants.Accession.SUBTAXA) != null
-					|| accnJson.get(Api1Constants.Accession.SUBTAUTHOR) != null) {
+			if (accession.getAccessionId().isPersisted() || useUniqueAcceNumbs && accnJson.get(Api1Constants.Accession.GENUS) != null || accnJson.get(
+				Api1Constants.Accession.GENUS_NEW) != null || accnJson.get(Api1Constants.Accession.SPECIES) != null || accnJson.get(Api1Constants.Accession.SPAUTHOR) != null || accnJson
+					.get(Api1Constants.Accession.SUBTAXA) != null || accnJson.get(Api1Constants.Accession.SUBTAUTHOR) != null) {
 
 				updateTaxonomy(accession, accnJson);
 			}
 
+			updateDoi(accession, accnJson.get(Api1Constants.Accession.DOI));
+			if (accession.getDoi()!=null) {
+				// Update ACCENUMB if DOI is provided
+				accession.setAccessionName(dataJson.acceNumb);
+			}
 			updateCrop(accession, accnJson.get(Api1Constants.Accession.CROPNAME));
 			updateAcceNumb(accession, accnJson.get(Api1Constants.Accession.ACCENUMB_NEW));
 			updateOrgCty(accession, accnJson.get(Api1Constants.Accession.ORIGCTY));
@@ -468,8 +471,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				}
 			}
 
-			if (accnJson.has(Api1Constants.Accession.DONORCODE) || accnJson.has(Api1Constants.Accession.DONORNUMB)
-					|| accnJson.has(Api1Constants.Accession.DONORNAME)) {
+			if (accnJson.has(Api1Constants.Accession.DONORCODE) || accnJson.has(Api1Constants.Accession.DONORNUMB) || accnJson.has(Api1Constants.Accession.DONORNAME)) {
 				AccessionExchange accnExch = genesysService.listAccessionExchange(accession.getAccessionId());
 				if (accnExch == null) {
 					accnExch = new AccessionExchange();
@@ -514,7 +516,6 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			upsertResponse.setResult(upsertResult);
 		}
 
-		
 		List<Accession> savedData = null;
 
 		if (toSave.size() > 0) {
@@ -524,8 +525,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			// Iterate savedData to extract UUIDs
 			upsertResponses.stream().forEach(response -> {
 				Accession accession = saved.stream().filter(a -> useUniqueAcceNumbs ? (a.getAccessionName().equalsIgnoreCase(response.getAcceNumb()))
-						: (a.getAccessionName().equalsIgnoreCase(response.getAcceNumb()) && a.getTaxonomy().getGenus().equalsIgnoreCase(response.getGenus())))
-						.findFirst().orElse(null);
+						: (a.getAccessionName().equalsIgnoreCase(response.getAcceNumb()) && a.getTaxonomy().getGenus().equalsIgnoreCase(response.getGenus()))).findFirst().orElse(null);
 
 				UpsertResult result = response.getResult();
 				if (accession != null) {
@@ -537,8 +537,8 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 					result.setUUID(accession.getUuid());
 				}
 			});
-			
-			savedData=saved;
+
+			savedData = saved;
 		}
 
 		if (toSaveColl.size() > 0) {
@@ -582,13 +582,52 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		updateAccessionAliases(collNumbs, AliasType.COLLNUMB, false);
 
 		LOG.info("Done saving data");
-		
+
 		// Update PDCI
 		genesysService.updatePDCI(savedData.stream().map(a -> a.getId()).collect(Collectors.toSet()));
-		
+
 		return upsertResponses;
 	}
 
+	/**
+	 * Update accession DOI in Genesys. If DOI exists in Genesys, it must be provided by the client and must match current value. If DOI does not exist in Genesys,
+	 * it will be registered.
+	 * 
+	 * @param accession
+	 * @param value
+	 * @return
+	 * @throws RESTApiException
+	 */
+	private boolean updateDoi(AccessionData accession, JsonNode value) throws RESTApiException {
+		if (accession.getDoi() == null) {
+			// Genesys does not have DOI for the accession
+			if (value != null) {
+				if (value.isTextual()) {
+					if (DOIUtils.isValidDoi(value.textValue())) {
+						accession.setDoi(value.textValue());
+						return true;
+					} else {
+						throw new RESTApiException("Invalid DOI value " + value.textValue());
+					}
+				} else {
+					throw new RESTApiDataTypeException("DOI must be a string.");
+				}
+			}
+			return false;
+		} else {
+			// Genesys has DOI for the accession
+			if (value == null || !value.isTextual()) {
+				throw new RESTApiException("DOI must be resubmitted for accession with DOI " + accession.getDoi() + " ACCENUMB=" + accession.getAccessionName());
+			} else {
+				if (StringUtils.equals(accession.getDoi(), value.textValue())) {
+					return false;
+				} else {
+					throw new RESTApiException("Provided DOI does not match existing DOI " + accession.getDoi() + " ACCENUMB=" + accession.getAccessionName());
+				}
+			}
+		}
+	}
+
 	private boolean updateCrop(Accession accession, JsonNode value) throws RESTApiDataTypeException {
 		if (value != null) {
 			if (value.isNull()) {
@@ -738,7 +777,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	private boolean updateAcceNumb(AccessionData accession, JsonNode value) throws RESTApiDataTypeException, RESTApiException {
 		if (value != null) {
 			// Rename is possible only if accession exists
-			if (! accession.getAccessionId().isPersisted()) {
+			if (!accession.getAccessionId().isPersisted()) {
 				throw new RESTApiException("Cannot rename a new accession entry");
 			}
 
@@ -787,10 +826,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	private boolean updateUuid(AccessionData accession, JsonNode value) throws RESTApiValueException {
 		// We don't allow UUID updates
 		/*
-		 * if (value != null) { final UUID uuid = value.isNull() ? null :
-		 * UUID.fromString(value.textValue());
-		 * 
-		 * if (accession.getUuid() == null && uuid != null) {
+		 * if (value != null) { final UUID uuid = value.isNull() ? null : UUID.fromString(value.textValue()); if (accession.getUuid() == null && uuid != null) {
 		 * accession.getAccessionId().setUuid(uuid); return true; } }
 		 */
 		// No change
@@ -827,12 +863,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 		Taxonomy2 ensuredTaxonomy = null;
 		try {
-			ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-					current.getSubtAuthor());
+			ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(), current.getSubtAuthor());
 		} catch (Throwable e) {
-			LOG.warn("*** lower(t.genus)=lower(" + current.getGenus() + ") and lower(t.species)=lower(" + current.getSpecies()
-					+ ") and lower(t.spauthor)=lower(" + current.getSpAuthor() + ") and lower(t.subtaxa)=lower(" + current.getSubtaxa()
-					+ ") and lower(subtauthor)=lower(" + current.getSubtAuthor() + ")");
+			LOG.warn("*** lower(t.genus)=lower(" + current.getGenus() + ") and lower(t.species)=lower(" + current.getSpecies() + ") and lower(t.spauthor)=lower(" + current.getSpAuthor()
+					+ ") and lower(t.subtaxa)=lower(" + current.getSubtaxa() + ") and lower(subtauthor)=lower(" + current.getSubtAuthor() + ")");
 		}
 
 		if (ensuredTaxonomy == null) {
@@ -1047,6 +1081,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		// Find aliases to remove
 		for (final AccessionAlias aa : existingAliases) {
 			if (null == CollectionUtils.find(aliases, new Predicate<AccessionAliasJson>() {
+
 				@Override
 				public boolean evaluate(AccessionAliasJson alias) {
 					return StringUtils.equals(alias.name, aa.getName());
@@ -1056,7 +1091,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			}
 		}
 		// Add or update
-		for (final AccessionAliasJson aa : aliases) {
+		for (
+
+		final AccessionAliasJson aa : aliases) {
 			AccessionAlias accessionAlias = CollectionUtils.find(existingAliases, new Predicate<AccessionAlias>() {
 				@Override
 				public boolean evaluate(AccessionAlias alias) {

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

@@ -283,7 +283,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 
 	@Override
 	public Page<AccessionDetails> listAccessionsDetails(Collection<Long> accessionIds, Pageable pageable) {
-		if (! accessionIds.isEmpty()) {
+		if (!accessionIds.isEmpty()) {
 			Page<Accession> data = accessionRepository.findById(accessionIds, pageable);
 			return new PageImpl<AccessionDetails>(getAccessionDetails(data.getContent().stream().map(a -> a.getId()).collect(Collectors.toList())), pageable, data.getTotalElements());
 		} else {
@@ -330,14 +330,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Override
 	public Accession getAccession(long accessionId) {
 		Accession accession = accessionRepository.findOne(accessionId);
-		if (accession != null) {
-			accession.getStoRage().size();
-			if (accession.getCountryOfOrigin() != null)
-				accession.getCountryOfOrigin().getId();
-			if (accession.getCrop() != null)
-				accession.getCrop().getId();
-		}
-		return accession;
+		return lazyLoadAccession(accession);
 	}
 
 	@Override
@@ -347,8 +340,13 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	private Accession lazyLoadAccession(Accession accession) {
-		if (accession != null)
+		if (accession != null) {
 			accession.getStoRage().size();
+			if (accession.getCountryOfOrigin() != null)
+				accession.getCountryOfOrigin().getId();
+			if (accession.getCrop() != null)
+				accession.getCrop().getId();
+		}
 		return accession;
 	}
 
@@ -854,8 +852,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	/**
-	 * Update {@link SvalbardDeposit} data and link with Genesys accessions. The primary key for {@link SvalbardDeposit}
-	 * is the <code>sgsv_id</code> as provided by NordGen.
+	 * Update {@link SvalbardDeposit} data and link with Genesys accessions. The primary key for {@link SvalbardDeposit} is the <code>sgsv_id</code> as provided by
+	 * NordGen.
 	 * 
 	 * Any existing SGSV records are first deleted. Inserted and linked with accessions in this method.
 	 * 
@@ -1180,7 +1178,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		final BufferedWriter osw = new BufferedWriter(new OutputStreamWriter(zos));
 		osw.write("<?xml version='1.0' encoding='utf-8'?>\n");
 		osw.write(
-				"<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
+			"<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
 		osw.write("<core encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 		osw.write("\t<files><location>core.csv</location></files>\n");
 		osw.write("\t<id index=\"0\" />\n");
@@ -1276,8 +1274,8 @@ 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", "doi" });
+		csv.writeNext(new String[] { "genesysId", "uuid", "instCode", "acceNumb", "genus", "species", "fullTaxa", "orgCty", "acqSrc", "acqDate", "mlsStat", "available", "historic",
+				"storage", "sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate", "doi" });
 
 		final ResultSetHelper csvResultsetHelper = new CSVResultSetHelper();
 
@@ -1448,7 +1446,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		final BufferedWriter osw = new BufferedWriter(new OutputStreamWriter(zos));
 		osw.write("<?xml version='1.0' encoding='utf-8'?>\n");
 		osw.write(
-				"<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
+			"<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
 		osw.write("<core encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 		osw.write("\t<files><location>core.csv</location></files>\n");
 		osw.write("\t<id index=\"0\" />\n");

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

@@ -49,6 +49,8 @@ import org.genesys2.server.service.impl.SearchException;
 import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
 import org.genesys2.spring.ResourceNotFoundException;
+import org.genesys2.util.DOIUtils;
+import org.genesys2.util.InvalidDOIException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.CannotAcquireLockException;
 import org.springframework.data.domain.Page;
@@ -109,8 +111,7 @@ public class AccessionController extends RestController {
 	 * @throws NonUniqueAccessionException
 	 */
 	@RequestMapping(value = "/exists/{instCode}/{genus:.+}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody boolean exists(@PathVariable("instCode") String instCode, @PathVariable("genus") String genus,
-			@RequestParam("acceNumb") String acceNumb) throws NonUniqueAccessionException {
+	public @ResponseBody boolean exists(@PathVariable("instCode") String instCode, @PathVariable("genus") String genus, @RequestParam("acceNumb") String acceNumb) throws NonUniqueAccessionException {
 		if (LOG.isDebugEnabled()) {
 			LOG.debug("Checking if accn exists " + instCode + "." + acceNumb + " genus=" + genus);
 		}
@@ -195,8 +196,7 @@ public class AccessionController extends RestController {
 	 * @throws RESTApiException
 	 */
 	@RequestMapping(value = "/{instCode}/upsert", method = { RequestMethod.POST, RequestMethod.PUT }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody Object upsertInstituteAccession(@PathVariable("instCode") String instCode, @RequestBody String content)
-			throws JsonProcessingException, IOException, RESTApiException {
+	public @ResponseBody Object upsertInstituteAccession(@PathVariable("instCode") String instCode, @RequestBody String content) throws JsonProcessingException, IOException, RESTApiException {
 
 		// User's permission to WRITE to this WIEWS institute are checked in
 		// BatchRESTService.
@@ -210,18 +210,26 @@ public class AccessionController extends RestController {
 
 		if (json.isArray()) {
 			for (final JsonNode j : json) {
-				final AccessionHeaderJson dataJson = readAid3(j);
-				if (!instCode.equals(dataJson.instCode)) {
-					throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
+				try {
+					final AccessionHeaderJson dataJson = readAid3(j);
+					if (!instCode.equals(dataJson.instCode)) {
+						throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
+					}
+					batch.put(dataJson, (ObjectNode) j);
+				} catch (InvalidDOIException e) {
+					throw new RESTApiException("Invalid DOI", e);
 				}
-				batch.put(dataJson, (ObjectNode) j);
 			}
 		} else {
-			final AccessionHeaderJson dataJson = readAid3(json);
-			if (!instCode.equals(dataJson.instCode)) {
-				throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
+			try {
+				final AccessionHeaderJson dataJson = readAid3(json);
+				if (!instCode.equals(dataJson.instCode)) {
+					throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
+				}
+				batch.put(dataJson, (ObjectNode) json);
+			} catch (InvalidDOIException e) {
+				throw new RESTApiException("Invalid DOI", e);
 			}
-			batch.put(dataJson, (ObjectNode) json);
 		}
 
 		Throwable cause = null;
@@ -295,10 +303,8 @@ public class AccessionController extends RestController {
 	 * @throws IOException
 	 * @throws JsonProcessingException
 	 */
-	@RequestMapping(value = "/{instCode}/names", method = { RequestMethod.POST, RequestMethod.PUT }, consumes = {
-			MediaType.APPLICATION_JSON_VALUE }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody List<AccessionOpResponse> upsertAccessionNames(@PathVariable("instCode") String instCode, @RequestBody List<AccessionNamesJson> batch)
-			throws RESTApiException {
+	@RequestMapping(value = "/{instCode}/names", method = { RequestMethod.POST, RequestMethod.PUT }, consumes = { MediaType.APPLICATION_JSON_VALUE }, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody List<AccessionOpResponse> upsertAccessionNames(@PathVariable("instCode") String instCode, @RequestBody List<AccessionNamesJson> batch) throws RESTApiException {
 		// User's permission to WRITE to this WIEWS institute are checked in
 		// BatchRESTService.
 		final FaoInstitute institute = instituteService.getInstitute(instCode);
@@ -357,10 +363,9 @@ public class AccessionController extends RestController {
 	 * @throws IOException
 	 * @throws JsonProcessingException
 	 */
-	@RequestMapping(value = "/{instCode}/delete-named", method = { RequestMethod.POST, RequestMethod.PUT }, consumes = {
-			MediaType.APPLICATION_JSON_VALUE }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody List<AccessionOpResponse> deleteAccessions(@PathVariable("instCode") String instCode, @RequestBody List<AccessionHeaderJson> batch)
-			throws RESTApiException {
+	@RequestMapping(value = "/{instCode}/delete-named", method = { RequestMethod.POST, RequestMethod.PUT }, consumes = { MediaType.APPLICATION_JSON_VALUE }, produces = {
+			MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody List<AccessionOpResponse> deleteAccessions(@PathVariable("instCode") String instCode, @RequestBody List<AccessionHeaderJson> batch) throws RESTApiException {
 		// User's permission to WRITE to this WIEWS institute are checked in
 		// BatchRESTService.
 		final FaoInstitute institute = instituteService.getInstitute(instCode);
@@ -422,8 +427,7 @@ public class AccessionController extends RestController {
 	 * @throws IOException
 	 * @throws JsonProcessingException
 	 */
-	@RequestMapping(value = "/{instCode}/delete", method = { RequestMethod.POST }, consumes = { MediaType.APPLICATION_JSON_VALUE }, produces = {
-			MediaType.APPLICATION_JSON_VALUE })
+	@RequestMapping(value = "/{instCode}/delete", method = { RequestMethod.POST }, consumes = { MediaType.APPLICATION_JSON_VALUE }, produces = { MediaType.APPLICATION_JSON_VALUE })
 	public @ResponseBody int deleteAccessionsById(@PathVariable("instCode") String instCode, @RequestBody List<Long> batch) throws RESTApiException {
 		// User's permission to WRITE to this WIEWS institute are checked in
 		// BatchRESTService.
@@ -445,8 +449,7 @@ public class AccessionController extends RestController {
 
 	// FIXME Not using institute...
 	@RequestMapping(value = "/{instCode}/list", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody Page<AccessionDetails> list(@PathVariable("instCode") String instCode, @RequestParam("page") int page,
-			@RequestParam("query") String query) throws SearchException {
+	public @ResponseBody Page<AccessionDetails> list(@PathVariable("instCode") String instCode, @RequestParam("page") int page, @RequestParam("query") String query) throws SearchException {