Taxonomy to Taxonomy2

src/main/java/org/genesys2/server/listener/sample/TaxonomyUpgrade.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.listener.sample;
+
+import java.util.List;
+import java.util.concurrent.atomic.AtomicLong;
+
+import org.genesys2.server.listener.RunAsAdminListener;
+import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.persistence.domain.GenesysLowlevelRepository;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.TaxonomyService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+/**
+ * Upgrades taxonomy1 to taxonomy2
+ * 
+ * @author mobreza
+ */
+@Component
+public class TaxonomyUpgrade extends RunAsAdminListener {
+
+	@Autowired
+	GenesysService genesysService;
+
+	@Autowired
+	GenesysLowlevelRepository genesysLowlevelRepository;
+
+	@Autowired
+	TaxonomyService taxonomyService;
+
+	@Override
+	public void init() throws Exception {
+		_logger.info("Checking if default content exists");
+
+		long count = taxonomyService.countTaxonomy2();
+		_logger.warn("Taxonomy2 count=" + count);
+
+		if (count != 0) {
+			_logger.warn("Not changing taxonomy2");
+			return;
+		}
+
+		final AtomicLong counter = new AtomicLong(0);
+
+		List<Taxonomy> oldTaxa = taxonomyService.findAll();
+		for (Taxonomy t1 : oldTaxa) {
+			String genus = t1.getGenus();
+			String species = t1.getSpecies();
+
+			String spAuthor = null;
+			String subtaxa = null;
+			String subtAuthor = null;
+
+			// Make new taxonomy
+			Taxonomy2 t2 = taxonomyService.ensureTaxonomy2(genus, species, spAuthor, subtaxa, subtAuthor);
+
+			// Update all accessions
+			count = taxonomyService.upgradeTaxonomy(t1, t2);
+			_logger.info("Upgraded " + t1 + " to " + t2 + " on accessions=" + count);
+		}
+
+		_logger.warn("Updated Taxonomy2 count=" + counter);
+	}
+}

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

@@ -97,7 +97,7 @@ public class Accession extends VersionedAuditedModel {
 	private Boolean mlsStatus;
 
 	@Column(name = "taxGenus", nullable = true)
-	private long taxGenus;
+	private Long taxGenus;
 
 	@Column(name = "taxSpecies", nullable = true)
 	private Long taxSpecies;
@@ -237,7 +237,8 @@ public class Accession extends VersionedAuditedModel {
 		return taxGenus;
 	}
 
-	public void setTaxGenus(long taxGenus) {
+	// TODO Must be long
+	public void setTaxGenus(Long taxGenus) {
 		this.taxGenus = taxGenus;
 	}
 

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

@@ -21,6 +21,7 @@ import java.text.MessageFormat;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.Lob;
+import javax.persistence.PrePersist;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
@@ -54,13 +55,18 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	@Lob
 	private String taxonName;
 
-	private long taxGenus;
+	private Long taxGenus;
 
 	private Long taxSpecies;
 
 	// @OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
 	// private List<CropTaxonomy> cropTaxonomies;
 
+	@PrePersist
+	private void prePersist() {
+		this.taxonName = getTaxonName();
+	}
+
 	public String getGenus() {
 		return this.genus;
 	}
@@ -91,7 +97,7 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 
 	public void setTaxonName(String taxonName) {
 		// Ignore what they provide
-		taxonName = getTaxonName();
+		this.taxonName = getTaxonName();
 	}
 
 	// public List<CropTaxonomy> getCropTaxonomies() {
@@ -130,11 +136,11 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 		return taxonomy == null ? false : taxonomy.getId().equals(id);
 	}
 
-	public long getTaxGenus() {
+	public Long getTaxGenus() {
 		return this.taxGenus;
 	}
 
-	public void setTaxGenus(long taxGenus) {
+	public void setTaxGenus(Long taxGenus) {
 		this.taxGenus = taxGenus;
 	}
 
@@ -148,7 +154,7 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 
 	@Override
 	public String toString() {
-		return MessageFormat.format("Tax id={0} taxonName=", id, getTaxonName());
+		return MessageFormat.format("Tax id={0} taxonName={1}", id, getTaxonName());
 	}
 
 }

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

@@ -35,7 +35,7 @@ import com.fasterxml.jackson.databind.annotation.JsonSerialize;
  * @author mobreza
  */
 @Entity
-@Table(name = "croprule", uniqueConstraints = { @UniqueConstraint(columnNames = { "cropId", "genus", "species" }) })
+@Table(name = "croprule", uniqueConstraints = { @UniqueConstraint(columnNames = { "cropId", "genus", "species", "subtaxa" }) })
 @JsonSerialize(using = CropRuleSerializer.class)
 public class CropRule extends BusinessModel {
 	private static final long serialVersionUID = -2336100072991067193L;
@@ -46,8 +46,11 @@ public class CropRule extends BusinessModel {
 	@Column(nullable = false, length = 100)
 	private String genus;
 
-	@Column
+	@Column(nullable = true, length = 100)
 	private String species;
+	
+	@Column(nullable = true, length = 100)
+	private String subtaxa;
 
 	@ManyToOne(cascade = {}, fetch = FetchType.EAGER, optional = false)
 	@JoinColumn(name = "cropId")
@@ -76,6 +79,14 @@ public class CropRule extends BusinessModel {
 	public void setSpecies(String species) {
 		this.species = species;
 	}
+	
+	public String getSubtaxa() {
+		return subtaxa;
+	}
+	
+	public void setSubtaxa(String subtaxa) {
+		this.subtaxa = subtaxa;
+	}
 
 	public Crop getCrop() {
 		return crop;

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

@@ -21,7 +21,7 @@ import java.util.List;
 import java.util.Set;
 
 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.FaoInstitute;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
@@ -41,6 +41,9 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query(countQuery = "select count(*) from accession a where a.taxGenus = ?1")
 	Page<Accession> findByTaxGenus(long taxonomyId, Pageable pageable);
 
+	@Query(countQuery = "select count(*) from accession a where a.taxSpecies = ?1")
+	Page<Accession> findByTaxSpecies(long taxSpecies, Pageable pageable);
+
 	List<Accession> findByInstitute(FaoInstitute institute);
 
 	@Query("select count(a) from Accession a where a.institute = ?1")
@@ -90,12 +93,12 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query("from Accession a where a.id in ( ?1 )")
 	List<Accession> listById(Collection<Long> accessionIds, Sort sort);
 
-	Page<Accession> findByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
+	Page<Accession> findByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy2 taxonomy, Pageable pageable);
 
-	Page<Accession> findByTaxonomy(Taxonomy taxonomy, Pageable pageable);
+	Page<Accession> findByTaxonomy(Taxonomy2 taxonomy, Pageable pageable);
 
 	@Query("select a from Accession a where a.taxonomy in ( ?1 )")
-	Page<Accession> findByTaxonomy(Collection<Taxonomy> taxonomies, Pageable pageable);
+	Page<Accession> findByTaxonomy(Collection<Taxonomy2> taxonomies, Pageable pageable);
 
 	Accession findByInstituteCodeAndAccessionName(String instCode, String accessionName);
 
@@ -109,4 +112,6 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query("update Accession a set a.inSvalbard = true where a in ?1")
 	void setInSvalbard(List<Accession> matching);
 
+	Page<Accession> findByInstituteAndTaxSpecies(FaoInstitute institute, long taxSpecies, Pageable pageable);
+
 }

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

@@ -39,6 +39,7 @@ public interface CropTaxonomyRepository extends JpaRepository<CropTaxonomy, Long
 
 	Page<CropTaxonomy> findByCrop(Crop crop, Pageable pageable);
 
+	// TODO FIXME todo
 	@Query("select distinct t from CropTaxonomy ct inner join ct.taxonomy t where ct.crop = ?1")
 	List<Taxonomy> findTaxonomiesByCrop(Crop crop);
 

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

@@ -51,4 +51,5 @@ public interface GenesysLowlevelRepository {
 	void listAccessionsAccenames(RowCallbackHandler rowCallbackHandler);
 
 	void listAccessionsAlias(RowCallbackHandler rowCallbackHandler);
+
 }

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

@@ -31,6 +31,5 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
 	@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);
+	Taxonomy2 findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
 }

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

@@ -19,8 +19,10 @@ package org.genesys2.server.persistence.domain;
 import java.util.List;
 
 import org.genesys2.server.model.genesys.Taxonomy;
+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.Modifying;
 import org.springframework.data.jpa.repository.Query;
 
 public interface TaxonomyRepository extends JpaRepository<Taxonomy, Long> {
@@ -35,4 +37,8 @@ public interface TaxonomyRepository extends JpaRepository<Taxonomy, Long> {
 
 	@Query("select distinct t.taxonName from Taxonomy t where t.taxonName like ?1")
 	List<String> autocompleteTaxonomy(String term, Pageable page);
+
+	@Modifying
+	@Query("update Accession a set a.taxonomy=?2, a.taxGenus=?3, a.taxSpecies=?4 where a.taxonomy1 = ?1")
+	int upgrade(Taxonomy t1, Taxonomy2 t2, Long taxGenus, Long taxSpecies);
 }

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

@@ -34,7 +34,6 @@ import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.SvalbardData;
-import org.genesys2.server.model.genesys.Taxonomy;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
@@ -103,9 +102,9 @@ public interface GenesysService {
 
 //	Page<Object[]> statisticsCropByInstitute(FaoInstitute faoInstitute, Pageable pageable);
 
-	Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
+	Page<Accession> listAccessionsByInstituteAndSpecies(FaoInstitute institute, long taxSpecies, Pageable pageable);
 
-	Page<Accession> listAccessionsByTaxonomy(Taxonomy taxonomy, Pageable pageable);
+	Page<Accession> listAccessionsByTaxSpecies(long taxSpeciesId, Pageable pageable);
 
 	Page<Accession> listAccessionsByGenus(String genus, Pageable pageable);
 

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

@@ -25,9 +25,8 @@ public interface TaxonomyService {
 
 	Taxonomy get(String genus, String species);
 
-	Taxonomy ensureTaxonomy(String genus, String species); // , String
-															// fullTaxa);
-
+	Taxonomy ensureTaxonomy(String genus, String species);
+	
 	List<String> autocompleteGenus(String term);
 
 	List<String> autocompleteTaxonomy(String term);
@@ -38,4 +37,10 @@ public interface TaxonomyService {
 
 	Taxonomy2 ensureTaxonomy2(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
 
+	long countTaxonomy2();
+
+	List<Taxonomy> findAll();
+
+	long upgradeTaxonomy(Taxonomy t1, Taxonomy2 t2);
+
 }

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

@@ -70,6 +70,7 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
 
 @Service
 @Transactional(readOnly = true)
+// FIXME TODO Change taxonomy to taxonomy2
 public class GenesysFilterServiceImpl implements GenesysFilterService {
 
 	private static final Log LOG = LogFactory.getLog(GenesysFilterServiceImpl.class);

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

@@ -53,7 +53,7 @@ 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.genesys.SvalbardData;
-import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.genesys.TraitCode;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.model.impl.Country;
@@ -367,13 +367,13 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	}
 
 	@Override
-	public Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable) {
-		return accessionRepository.findByInstituteAndTaxonomy(institute, taxonomy, pageable);
+	public Page<Accession> listAccessionsByInstituteAndSpecies(FaoInstitute institute, long taxSpecies, Pageable pageable) {
+		return accessionRepository.findByInstituteAndTaxSpecies(institute, taxSpecies, pageable);
 	}
 
 	@Override
-	public Page<Accession> listAccessionsByTaxonomy(Taxonomy taxonomy, Pageable pageable) {
-		return accessionRepository.findByTaxonomy(taxonomy, pageable);
+	public Page<Accession> listAccessionsByTaxSpecies(long taxSpecies, Pageable pageable) {
+		return accessionRepository.findByTaxSpecies(taxSpecies, pageable);
 	}
 
 	@Override
@@ -389,7 +389,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 
 	@Override
 	public Page<Accession> listAccessionsByCrop(Crop crop, Pageable pageable) {
-		List<Taxonomy> taxonomies = cropTaxonomyRepository.findTaxonomiesByCrop(crop);
+		List<Taxonomy2> taxonomies = null;// FIXME TODO cropTaxonomyRepository.findTaxonomiesByCrop(crop);
 		if (taxonomies == null || taxonomies.size() == 0) {
 			return null;
 		}

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

@@ -19,6 +19,7 @@ package org.genesys2.server.service.impl;
 import java.util.List;
 
 import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.text.WordUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Taxonomy;
@@ -39,6 +40,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	@Autowired
 	private TaxonomyRepository taxonomyRepository;
 
+	@Autowired
 	private Taxonomy2Repository taxonomy2Repository;
 
 	@Override
@@ -62,14 +64,16 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 		Taxonomy taxonomy = taxonomyRepository.getByGenusAndSpecies(genus, species);
 		if (taxonomy == null) {
 			taxonomy = new Taxonomy();
-			LOG.warn("Inserting " + genus + " " + species);
+			if (LOG.isDebugEnabled())
+				LOG.debug("Inserting " + genus + " " + species);
+
 			taxonomy.setGenus(genus);
 			taxonomy.setSpecies(species);
 			taxonomy.setTaxonName((genus + " " + StringUtils.defaultIfEmpty(species, "")).trim());
 
 			try {
 				taxonomyRepository.save(taxonomy);
-				LOG.warn("Inserted new:" + taxonomy);
+				LOG.info("Inserted new:" + taxonomy);
 
 				// TODO Should update crop taxonomy lists?
 
@@ -91,16 +95,36 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	}
 
 	@Override
+	// @Transactional(noRollbackFor = AssertionFailure.class)
 	@Transactional
 	public Taxonomy2 ensureTaxonomy2(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) {
-		if (species == null && spAuthor != null) {
+		if (StringUtils.isBlank(genus)) {
+			throw new RuntimeException("Genus can't be blank");
+		}
+
+		// Capitalize
+		genus = WordUtils.capitalizeFully(genus);
+
+		species = StringUtils.defaultIfBlank(species, "sp.");
+		species = species.toLowerCase();
+
+		spAuthor = StringUtils.defaultIfBlank(spAuthor, null);
+		subtaxa = StringUtils.defaultIfBlank(subtaxa, null);
+
+		if (subtaxa != null)
+			subtaxa = subtaxa.toLowerCase();
+
+		subtAuthor = StringUtils.defaultIfBlank(subtAuthor, null);
+
+		if (StringUtils.equalsIgnoreCase(species.trim(), "sp")) {
 			species = "sp.";
 		}
-		if (subtaxa == null && subtAuthor != null) {
+
+		if (StringUtils.isNotBlank(species) && !StringUtils.equals(species, "sp.") && StringUtils.isBlank(subtaxa)) {
 			subtaxa = "subsp.";
 		}
 
-		Taxonomy2 existing = taxonomy2Repository.findOne(genus, species, spAuthor, subtaxa, subtAuthor);
+		Taxonomy2 existing = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, spAuthor, subtaxa, subtAuthor);
 		if (existing == null) {
 			return internalEnsure(genus, species, spAuthor, subtaxa, subtAuthor);
 		}
@@ -108,12 +132,26 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	}
 
 	private synchronized Taxonomy2 internalEnsure(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) {
+		Taxonomy2 genusTaxa = null;
+		Taxonomy2 speciesTaxa = null;
+		if (species != null && !StringUtils.equals(species, "sp.") && (subtaxa != null || spAuthor != null || subtAuthor != null)) {
+			genusTaxa = internalEnsure(genus, "sp.", null, null, null);
+		}
+		if (species != null && !StringUtils.equals(species, "sp.") && !StringUtils.equals(subtaxa, "subsp.") && spAuthor != null && subtAuthor != null) {
+			speciesTaxa = internalEnsure(genus, species, null, "subsp.", null);
+		}
+
 		// Loop it a bit if required
 		for (int i = 5; i > 0; i--) {
-			Taxonomy2 taxonomy = taxonomy2Repository.findOne(genus, species, spAuthor, subtaxa, subtAuthor);
+			Taxonomy2 taxonomy = null;
+			try {
+				taxonomy = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, spAuthor, subtaxa, subtAuthor);
+			} catch (Throwable e) {
+				// is null
+				e.printStackTrace();
+			}
 			if (taxonomy == null) {
 				taxonomy = new Taxonomy2();
-				LOG.warn("Inserting new taxonomy");
 				taxonomy.setGenus(genus);
 				taxonomy.setSpecies(species);
 				taxonomy.setSpAuthor(spAuthor);
@@ -121,35 +159,31 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 				taxonomy.setSubtAuthor(subtAuthor);
 
 				try {
-					taxonomy = taxonomy2Repository.save(taxonomy);
-					LOG.warn("Inserted new:" + taxonomy);
-
-					if (!StringUtils.equals(species, "sp.") && spAuthor != null && subtaxa != null && subtAuthor != null) {
-						Taxonomy2 genusTaxa = internalEnsure(genus, "sp.", null, null, null);
+					if (genusTaxa != null) {
 						taxonomy.setTaxGenus(genusTaxa.getId());
-
-						if (species != null && subtaxa != null && !StringUtils.equals(subtaxa, "subsp.") && subtAuthor != null) {
-							Taxonomy2 speciesTaxa = internalEnsure(genus, species, null, "subsp.", null);
-							taxonomy.setTaxSpecies(speciesTaxa.getId());
-						} else {
-							// No species taxonomy
-						}
-
 					} else {
+						taxonomy = taxonomy2Repository.save(taxonomy);
 						taxonomy.setTaxGenus(taxonomy.getId());
 					}
 
+					if (speciesTaxa != null) {
+						taxonomy.setTaxSpecies(speciesTaxa.getId());
+					} else {
+						taxonomy = taxonomy2Repository.save(taxonomy);
+						taxonomy.setTaxSpecies(taxonomy.getId());
+					}
+
 					taxonomy = taxonomy2Repository.save(taxonomy);
 
 					// TODO Should update crop taxonomy lists?
 
-					return taxonomy;
-
 				} catch (Throwable e) {
 					LOG.warn("Error " + e.getMessage() + " :" + taxonomy);
 					continue;
 				}
 			}
+
+			return taxonomy;
 		}
 
 		// Should not get here!
@@ -158,11 +192,29 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 
 	@Override
 	public long getTaxonomy2Id(String genus) {
-		return taxonomy2Repository.findOne(genus, "sp.", null, null, null).getId();
+		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, "sp.", null, null, null).getId();
 	}
 
 	@Override
 	public long getTaxonomy2Id(String genus, String species) {
-		return taxonomy2Repository.findOne(genus, species, null, "subsp.", null).getId();
+		Taxonomy2 tax = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, null, "subsp.", null);
+		System.err.println("tax2=" + tax);
+		return tax.getId();
+	}
+
+	@Override
+	public long countTaxonomy2() {
+		return taxonomy2Repository.count();
+	}
+
+	@Override
+	public List<Taxonomy> findAll() {
+		return taxonomyRepository.findAll();
+	}
+
+	@Override
+	@Transactional
+	public long upgradeTaxonomy(Taxonomy t1, Taxonomy2 t2) {
+		return taxonomyRepository.upgrade(t1, t2, t2.getTaxGenus(), t2.getTaxSpecies());
 	}
 }

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

@@ -20,7 +20,6 @@ import java.util.HashMap;
 import java.util.List;
 
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.Taxonomy;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysService;
@@ -159,22 +158,19 @@ public class AccessionController extends BaseController {
 			@RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 
 		// Taxonomy
-		Taxonomy taxonomy = taxonomyService.get(genus, species);
+		long taxSpeciesId = taxonomyService.getTaxonomy2Id(genus, species);
 
 		HashMap<Object, Object> filters = new HashMap<Object, Object>();
 		model.addAttribute("filters", filters);
 
-		_logger.debug("Got " + taxonomy);
-		filters.put("filter.taxonomy", taxonomy);
+		filters.put("filter.taxonomy", taxSpeciesId);
 
-		Page<Accession> accessions = genesysService.listAccessionsByTaxonomy(taxonomy, new PageRequest(page - 1, 50, new Sort("accessionName")));
+		Page<Accession> accessions = genesysService.listAccessionsByTaxSpecies(taxSpeciesId, new PageRequest(page - 1, 50, new Sort("accessionName")));
 
 		_logger.info("Got: " + accessions);
 		model.addAttribute("pagedData", accessions);
 
-		if (taxonomy != null) {
-			model.addAttribute("jsonFilter", "{\"taxon\":[\"" + taxonomy.getTaxonName() + "\"]}");
-		}
+		model.addAttribute("jsonFilter", "{\"species\":[\"" + taxSpeciesId + "\"]}");
 
 		return "/accession/data";
 	}

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

@@ -24,7 +24,6 @@ import java.util.Map;
 import javax.servlet.http.HttpServletResponse;
 
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.Taxonomy;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.ContentService;
 import org.genesys2.server.service.GenesysService;
@@ -177,21 +176,21 @@ public class WiewsController extends BaseController {
 		model.addAttribute("faoInstitute", faoInstitute);
 
 		// Taxonomy
-		Taxonomy taxonomy = taxonomyService.get(genus, species);
-		_logger.debug("Got " + taxonomy);
+		long taxonomyId = taxonomyService.getTaxonomy2Id(genus, species);
+		_logger.debug("Got " + taxonomyId);
 
 		_logger.warn("Searching accessions of: " + faoInstitute);
-		Page<Accession> accessions = genesysService.listAccessionsByInstituteAndTaxonomy(faoInstitute, taxonomy, new PageRequest(page - 1, 50, new Sort(
+		Page<Accession> accessions = genesysService.listAccessionsByInstituteAndSpecies(faoInstitute, taxonomyId, new <