New taxonomy

src/main/java/org/genesys2/server/lucene/genesys/AccessionBridge.java

@@ -21,7 +21,7 @@ import org.apache.commons.logging.LogFactory;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.hibernate.search.bridge.FieldBridge;
@@ -51,7 +51,7 @@ public class AccessionBridge implements FieldBridge {
 			sd.append(countryOfOrigin.getName());
 		}
 
-		Taxonomy taxonomy = accession.getTaxonomy();
+		Taxonomy2 taxonomy = accession.getTaxonomy();
 		if (taxonomy != null) {
 			sd.append(taxonomy.getTaxonName());
 		}

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

@@ -135,18 +135,14 @@ public class Accession extends VersionedAuditedModel {
 		this.accessionName = accessionName;
 	}
 
-	public Taxonomy getTaxonomy() {
+	public Taxonomy getTaxonomy1() {
 		return this.taxonomy;
 	}
 
-	public Taxonomy2 getTaxonomy2() {
+	public Taxonomy2 getTaxonomy() {
 		return this.taxonomy2;
 	}
-
-	public void setTaxonomy(final Taxonomy taxonomy) {
-		this.taxonomy = taxonomy;
-	}
-
+	
 	public String getAcquisitionSource() {
 		return this.acquisitionSource;
 	}
@@ -252,7 +248,7 @@ public class Accession extends VersionedAuditedModel {
 		this.taxSpecies = taxSpecies;
 	}
 
-	public void setTaxonomy2(Taxonomy2 taxonomy2) {
+	public void setTaxonomy(Taxonomy2 taxonomy2) {
 		this.taxonomy2 = taxonomy2;
 	}
 

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

@@ -20,6 +20,7 @@ import java.text.MessageFormat;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.Lob;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
@@ -49,6 +50,14 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	@Column(nullable = true, length = 100)
 	private String subtAuthor;
 
+	@Column(nullable = false)
+	@Lob
+	private String taxonName;
+
+	private long taxGenus;
+
+	private Long taxSpecies;
+
 	// @OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
 	// private List<CropTaxonomy> cropTaxonomies;
 
@@ -80,6 +89,11 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 		return sb.toString();
 	}
 
+	public void setTaxonName(String taxonName) {
+		// Ignore what they provide
+		taxonName = getTaxonName();
+	}
+
 	// public List<CropTaxonomy> getCropTaxonomies() {
 	// return cropTaxonomies;
 	// }
@@ -88,13 +102,53 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	// this.cropTaxonomies = cropTaxonomies;
 	// }
 
-	@Override
-	public String toString() {
-		return MessageFormat.format("Tax id={0} taxonName=", id, getTaxonName());
+	public String getSpAuthor() {
+		return spAuthor;
+	}
+
+	public void setSpAuthor(String spAuthor) {
+		this.spAuthor = spAuthor;
+	}
+
+	public String getSubtaxa() {
+		return subtaxa;
+	}
+
+	public void setSubtaxa(String subtaxa) {
+		this.subtaxa = subtaxa;
+	}
+
+	public String getSubtAuthor() {
+		return subtAuthor;
+	}
+
+	public void setSubtAuthor(String subtAuthor) {
+		this.subtAuthor = subtAuthor;
 	}
 
 	public boolean sameAs(Taxonomy2 taxonomy) {
 		return taxonomy == null ? false : taxonomy.getId().equals(id);
 	}
 
+	public long getTaxGenus() {
+		return this.taxGenus;
+	}
+
+	public void setTaxGenus(long taxGenus) {
+		this.taxGenus = taxGenus;
+	}
+
+	public Long getTaxSpecies() {
+		return this.taxSpecies;
+	}
+
+	public void setTaxSpecies(Long taxSpecies) {
+		this.taxSpecies = taxSpecies;
+	}
+
+	@Override
+	public String toString() {
+		return MessageFormat.format("Tax id={0} taxonName=", id, getTaxonName());
+	}
+
 }

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

@@ -24,6 +24,7 @@ import javax.persistence.Table;
 import org.genesys2.server.model.BusinessModel;
 import org.genesys2.server.model.genesys.Taxonomy;
 
+// TODO FIXME Need to link to {@link Taxonomy2}
 @Entity
 @Table(name = "croptaxonomy")
 public class CropTaxonomy extends BusinessModel {

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

@@ -87,6 +87,7 @@ public class FaoInstitute extends BusinessModel implements GeoReferencedEntity,
 	private Double latitude;
 	private Double longitude;
 	private Double elevation;
+	private boolean uniqueAcceNumbs;
 
 	public FaoInstitute() {
 	}
@@ -210,4 +211,12 @@ public class FaoInstitute extends BusinessModel implements GeoReferencedEntity,
 	public void setSettings(Map<String, FaoInstituteSetting> settings) {
 		this.settings = settings;
 	}
+
+	public boolean hasUniqueAcceNumbs() {
+		return this.uniqueAcceNumbs;
+	}
+	
+	public void setUniqueAcceNumbs(boolean uniqueAcceNumbs) {
+		this.uniqueAcceNumbs = uniqueAcceNumbs;
+	}
 }

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

@@ -96,8 +96,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query("select a from Accession a where a.taxonomy in ( ?1 )")
 	Page<Accession> findByTaxonomy(Collection<Taxonomy> taxonomies, Pageable pageable);
 
-	// Accession findByInstituteCodeAndAccessionName(String holdingInstitute,
-	// String accessionName);
+	Accession findByInstituteCodeAndAccessionName(String instCode, String acceNumb);
 
 	Accession findByInstituteCodeAndAccessionNameAndGenus(String holdingInstitute, String accessionName, String genus);
 

src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java

+/**
+ * Copyright 2014 Global Crop Diversity Trust
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
+package org.genesys2.server.persistence.domain;
+
+import java.util.List;
+
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+
+public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
+
+	@Query("select distinct t.genus from Taxonomy2 t where t.genus like ?1")
+	List<String> autocompleteGenus(String term, Pageable page);
+
+	@Query("select distinct t.taxonName from Taxonomy2 t where t.taxonName like ?1")
+	List<String> autocompleteTaxonomy(String term, Pageable page);
+
+	@Query("select t from Taxonomy2 t where t.genus=?1 and t.species=?2 and t.spAuthor=?3 and t.subtaxa=?4 and t.subtAuthor=?5")
+	Taxonomy2 findOne(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
+}

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

@@ -20,6 +20,7 @@ import java.util.List;
 import java.util.Map;
 
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.impl.RESTApiException;
 import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
 
@@ -27,7 +28,7 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
 
 public interface BatchRESTService {
 
-	boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch);
+	boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch) throws RESTApiException;
 
 	void upsertAccessionNames(FaoInstitute institute, List<AccessionNamesJson> batch);
 

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

@@ -20,6 +20,7 @@ import java.util.List;
 import java.util.Locale;
 
 import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.CropRule;
 import org.genesys2.server.model.impl.CropTaxonomy;
@@ -36,6 +37,8 @@ public interface CropService {
 
 	List<Crop> getCrops(Taxonomy taxonomy);
 
+	List<Crop> getCrops(Taxonomy2 taxonomy2);
+
 	void rebuildTaxonomies();
 
 	Page<CropTaxonomy> getCropTaxonomies(Crop crop, Pageable pageable);

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

@@ -95,7 +95,7 @@ public interface GenesysService {
 
 	Accession getAccession(AccessionIdentifier3 aid3);
 
-	Accession getAccession(String instCode, String genus, String acceNumb);
+	Accession getAccession(String instCode, String acceNumb, String genus);
 
 	Page<Object[]> statisticsGenusByInstitute(FaoInstitute faoInstitute, Pageable pageable);
 
@@ -163,4 +163,13 @@ public interface GenesysService {
 
 	long countAll();
 
+	/**
+	 * For institutes with {@link FaoInstitute#uniqueAcceNumbs}
+	 * 
+	 * @param instCode
+	 * @param acceNumb
+	 * @return the 1 accession
+	 */
+	Accession getAccession(String instCode, String acceNumb);
+
 }

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

@@ -19,6 +19,7 @@ package org.genesys2.server.service;
 import java.util.List;
 
 import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.Taxonomy2;
 
 public interface TaxonomyService {
 
@@ -31,4 +32,10 @@ public interface TaxonomyService {
 
 	List<String> autocompleteTaxonomy(String term);
 
+	long getTaxonomy2Id(String genus);
+
+	long getTaxonomy2Id(String genus, String species);
+
+	Taxonomy2 ensureTaxonomy2(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
+
 }

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

@@ -36,7 +36,7 @@ import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionExchange;
 import org.genesys2.server.model.genesys.AccessionGeo;
-import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.BatchRESTService;
@@ -81,8 +81,11 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
-	public boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch) {
+	public boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch) throws RESTApiException {
 		LOG.info("Batch processing " + batch.size() + " entries for " + institute);
+
+		boolean useUniqueAcceNumbs = institute.hasUniqueAcceNumbs();
+
 		List<Accession> toSave = new ArrayList<Accession>();
 		List<AccessionCollect> toSaveColl = new ArrayList<AccessionCollect>();
 		List<AccessionGeo> toSaveGeo = new ArrayList<AccessionGeo>();
@@ -102,94 +105,39 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				throw new RuntimeException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
 			}
 
-			Accession accession = genesysService.getAccession(dataJson.instCode, dataJson.genus, dataJson.acceNumb);
+			Accession accession = null;
+			if (useUniqueAcceNumbs)
+				accession = genesysService.getAccession(dataJson.instCode, dataJson.acceNumb);
+			else
+				accession = genesysService.getAccession(dataJson.instCode, dataJson.acceNumb, dataJson.genus);
 
 			boolean updated = false;
 
+			ObjectNode accnJson = batch.get(dataJson);
+
 			if (accession == null) {
 				LOG.warn("New accession " + dataJson);
 
 				accession = new Accession();
 				accession.setInstituteCode(dataJson.instCode);
 				accession.setInstitute(institute);
-				accession.setGenus(dataJson.genus);
 				accession.setAccessionName(dataJson.acceNumb);
 
-				updated = true;
-			}
-
-			ObjectNode accnJson = batch.get(dataJson);
-
-			JsonNode value = accnJson.get("orgCty");
-			if (value != null) {
-				String orgCty = value.textValue();
-				if (!StringUtils.equals(orgCty, accession.getOrigin())) {
-					Country country = geoService.getCountry(orgCty);
-					accession.setOrigin(orgCty);
-					accession.setCountryOfOrigin(country);
-					updated = true;
-				}
-			}
-
-			/* Allow updating AcceNumb */
-			value = accnJson.get("newAcceNumb");
-			if (value != null) {
-				String newAcceNumb = value.isNull() ? null : value.textValue();
-				if (!StringUtils.equals(newAcceNumb, accession.getAccessionName())) {
-					accession.setAccessionName(newAcceNumb);
-					updated = true;
-				}
-			}
-
-			/* Allow updating Genus */
-			value = accnJson.get("newGenus");
-			if (value != null) {
-				String newGenus = value.isNull() ? null : value.textValue();
-				if (!StringUtils.equals(newGenus, accession.getGenus())) {
-					accession.setGenus(newGenus);
-					updated = true;
-
-					// Need to do taxonomy
-					String species = null;
-					if (accession.getTaxonomy() != null)
-						species = accession.getTaxonomy().getSpecies();
-
-					value = accnJson.get("species");
-					if (value != null) {
-						species = value.isNull() ? null : value.textValue();
-					}
-
-					Taxonomy taxonomy = taxonomyService.ensureTaxonomy(accession.getGenus(), species);
-					if (!taxonomy.sameAs(accession.getTaxonomy())) {
-						accession.setTaxonomy(taxonomy);
-					}
+				if (accnJson.get("genus") == null || accnJson.get("newGenus") == null) {
+					throw new RESTApiException("Cannot create new accession without specifying genus");
 				}
-			}
 
-			value = accnJson.get("species");
-			if (value != null) {
-				String species = value.isNull() ? null : value.textValue();
-				Taxonomy taxonomy = taxonomyService.ensureTaxonomy(accession.getGenus(), species);
-				if (!taxonomy.sameAs(accession.getTaxonomy())) {
-					accession.setTaxonomy(taxonomy);
-					updated = true;
-				}
+				updated = true;
 			}
 
-			value = accnJson.get("uuid");
-			if (value != null) {
-				String uuid = value.isNull() ? null : value.textValue();
-				if (!StringUtils.equals(uuid, accession.getUuid())) {
-					if (uuid != null) {
-						// Throws a runtime exception if format is invalid
-						UUID.fromString(uuid);
-					}
-					accession.setUuid(uuid);
-					updated = true;
-				}
-			}
+			updated |= updateAcceNumb(accession, accnJson.get("newAcceNumb"));
+			updated |= updateTaxonomy(accession, accnJson);
+			updated |= updateOrgCty(accession, accnJson.get("orgCty"));
+			updated |= updateUuid(accession, accnJson.get("uuid"));
 
-			value = accnJson.get("acqDate");
+			// TODO Move other setters to methods
+			
+			JsonNode value = accnJson.get("acqDate");
 			if (value != null) {
 				String acqDate = value.isNull() ? null : value.textValue();
 				if (!StringUtils.equals(acqDate, accession.getAcquisitionDate())) {
@@ -417,6 +365,128 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		return toSave.size() > 0 || toSaveColl.size() > 0 || toSaveGeo.size() > 0 || toSaveBreed.size() > 0 || toSaveExch.size() > 0;
 	}
 
+	private boolean updateAcceNumb(Accession accession, JsonNode value) throws RESTApiDataTypeException, RESTApiValueException {
+		if (value != null) {
+			if (!value.isTextual()) {
+				throw new RESTApiDataTypeException("newAcceNumb must be a String");
+			}
+
+			if (value.isNull()) {
+				throw new RESTApiValueException("newAcceNumb cannot be null");
+			}
+
+			String newAcceNumb=value.textValue();
+			if (!StringUtils.equals(newAcceNumb, accession.getAccessionName())) {
+				accession.setAccessionName(newAcceNumb);
+				return true;
+			}
+		}
+		return false;
+	}
+
+	private boolean updateOrgCty(Accession accession, JsonNode value) throws RESTApiDataTypeException, RESTApiValueException {
+		if (value != null) {
+			if (!value.isNull() && !value.isTextual())
+				throw new RESTApiDataTypeException("orgCty must be a String");
+
+			String orgCty = value.textValue();
+			if (!StringUtils.equals(orgCty, accession.getOrigin())) {
+				Country country = null;
+				if (orgCty != null) {
+					country = geoService.getCountry(orgCty);
+					if (country == null)
+						throw new RESTApiValueException("No country with ISO3 code: " + orgCty);
+				}
+				accession.setOrigin(orgCty);
+				accession.setCountryOfOrigin(country);
+				return true;
+			}
+		}
+		return false;
+	}
+
+	private boolean updateUuid(Accession accession, JsonNode value) throws RESTApiValueException {
+		if (value != null) {
+			String uuid = value.isNull() ? null : value.textValue();
+			if (!StringUtils.equals(uuid, accession.getUuid())) {
+				if (uuid != null) {
+					try {
+						// Throws a runtime exception if format is invalid
+						UUID.fromString(uuid);
+					} catch (RuntimeException e) {
+						throw new RESTApiValueException("UUID " + uuid + " is not in valid format: " + e.getMessage());
+					}
+				}
+				accession.setUuid(uuid);
+				return true;
+			}
+		}
+		// No change
+		return false;
+	}
+
+	/**
+	 * Inspect incoming JSON and change taxonomy if required
+	 * 
+	 * @param accession
+	 * @param accnJson
+	 * 
+	 * @return true if taxonomy was modified
+	 * @throws RESTApiException
+	 */
+	private boolean updateTaxonomy(Accession accession, JsonNode accnJson) throws RESTApiException {
+		boolean updated = false;
+
+		// Do not persist this one, temporary use
+		Taxonomy2 current = accession.getTaxonomy();
+		if (current == null) {
+			current = new Taxonomy2();
+		}
+
+		// Load JSON values into "current"
+		current.setGenus(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("genus")), current.getGenus()));
+		current.setGenus(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("newGenus")), current.getGenus()));
+		current.setSpecies(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("species")), current.getSpecies()));
+		current.setSpAuthor(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("spauthor")), current.getSpAuthor()));
+		current.setSubtaxa(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("subtaxa")), current.getSubtaxa()));
+		current.setSubtAuthor(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("subtauthor")), current.getSubtAuthor()));
+
+		Taxonomy2 ensuredTaxonomy = null;
+		if (current.getId() == null
+				|| !((ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
+						current.getSubtAuthor())).sameAs(current))) {
+
+			accession.setTaxonomy(ensuredTaxonomy);
+			accession.setTaxGenus(ensuredTaxonomy.getTaxGenus());
+			accession.setTaxSpecies(ensuredTaxonomy.getTaxSpecies());
+
+			updated = true;
+		}
+
+		return updated;
+	}
+
+	/**
+	 * Return
+	 * 
+	 * @param jsonNode
+	 * @return
+	 * @throws RESTApiDataTypeException
+	 */
+	private String stringIfProvided(JsonNode jsonNode) throws RESTApiException {
+		if (jsonNode != null) {
+			if (!jsonNode.isTextual()) {
+				// We expect a String node
+				throw new RESTApiDataTypeException("Not a String");
+			}
+			if (StringUtils.isBlank(jsonNode.textValue())) {
+				throw new RESTApiValueException("Value cannot be a blank String");
+			}
+			return StringUtils.defaultIfBlank(jsonNode.textValue(), null);
+		}
+		return null;
+	}
+
 	private String arrayToString(ArrayNode arr) {
 		if (arr == null || arr.isNull())
 			return null;
@@ -514,7 +584,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		List<AccessionAlias> toRemove = new ArrayList<AccessionAlias>();
 
 		for (AccessionNamesJson dataJson : batch) {
-			Accession accession = genesysService.getAccession(institute.getCode(), dataJson.genus, dataJson.acceNumb);
+			Accession accession = genesysService.getAccession(institute.getCode(), dataJson.acceNumb, dataJson.genus);
 			if (accession == null) {
 				LOG.warn("No such accession " + dataJson);
 				continue;
@@ -599,7 +669,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				throw new RuntimeException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
 			}
 
-			Accession accession = genesysService.getAccession(dataJson.instCode, dataJson.genus, dataJson.acceNumb);
+			Accession accession = genesysService.getAccession(dataJson.instCode, dataJson.acceNumb, dataJson.genus);
 			if (accession != null) {
 				toDelete.add(accession);
 			}

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

@@ -26,6 +26,7 @@ import org.apache.commons.lang.StringUtils;