Accession#taxGenus, #taxSpecies removed, Taxonomy(1) removed

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

@@ -58,10 +58,6 @@ public class Accession extends VersionedAuditedModel {
 	@Column(name = "acceNumb", nullable = false, length = 128)
 	private String accessionName;
 
-//	@ManyToOne(cascade = {}, optional = true)
-//	@JoinColumn(name = "taxonomyId")
-//	private Taxonomy taxonomy1;
-
 //	@Cache(usage=CacheConcurrencyStrategy.READ_WRITE)
 	@ManyToOne(cascade = {}, optional = true)
 	@JoinColumn(name = "taxonomyId2")
@@ -98,12 +94,6 @@ public class Accession extends VersionedAuditedModel {
 	@Column(name = "mlsStat")
 	private Boolean mlsStatus;
 
-	@Column(name = "taxGenus", nullable = true)
-	private Long taxGenus;
-
-	@Column(name = "taxSpecies", nullable = true)
-	private Long taxSpecies;
-
 	@Column(name = "storage", nullable = false)
 	@ElementCollection(fetch = FetchType.LAZY)
 	@CollectionTable(name = "accessionstorage", joinColumns = @JoinColumn(name = "accessionId"))
@@ -241,23 +231,6 @@ public class Accession extends VersionedAuditedModel {
 		this.mlsStatus = mlsStatus;
 	}
 
-	public long getTaxGenus() {
-		return taxGenus == null ? -1 : taxGenus.longValue();
-	}
-
-	// TODO Must be long
-	public void setTaxGenus(Long taxGenus) {
-		this.taxGenus = taxGenus;
-	}
-
-	public Long getTaxSpecies() {
-		return taxSpecies;
-	}
-
-	public void setTaxSpecies(Long taxSpecies) {
-		this.taxSpecies = taxSpecies;
-	}
-
 	public void setTaxonomy(Taxonomy2 taxonomy2) {
 		this.taxonomy = taxonomy2;
 	}
@@ -288,6 +261,6 @@ public class Accession extends VersionedAuditedModel {
 
 	@Override
 	public String toString() {
-		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, taxGenus, accessionName);
+		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, "N/A", accessionName);
 	}
 }

src/main/java/org/genesys2/server/model/genesys/Taxonomy.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.model.genesys;
-
-import java.text.MessageFormat;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
-
-import org.genesys2.server.model.BusinessModel;
-
-@Entity
-// Add index on genus, genus+species
-@Table(name = "taxonomy", uniqueConstraints = { @UniqueConstraint(columnNames = { "genus", "species" }) })
-public class Taxonomy extends BusinessModel {
-
-	private static final long serialVersionUID = 8881324404490162933L;
-
-	@Column(nullable = false, length = 64)
-	private String genus;
-
-	@Column(nullable = false, length = 64)
-	private String species;
-
-	@Column(name = "taxonName", nullable = false, length = 200)
-	private String taxonName;
-
-	public String getGenus() {
-		return this.genus;
-	}
-
-	public void setGenus(final String genus) {
-		this.genus = genus;
-	}
-
-	public String getSpecies() {
-		return this.species;
-	}
-
-	public void setSpecies(final String species) {
-		this.species = species;
-	}
-
-	public String getTaxonName() {
-		return this.taxonName;
-	}
-
-	public void setTaxonName(final String taxonName) {
-		this.taxonName = taxonName;
-	}
-
-	@Override
-	public String toString() {
-		return MessageFormat.format("Tax id={0} genus={1} sp={2}, full={3}", id, genus, species, taxonName);
-	}
-
-	public boolean sameAs(Taxonomy taxonomy) {
-		return taxonomy == null ? false : taxonomy.getId().equals(id);
-	}
-
-}

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

@@ -39,21 +39,15 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query(countQuery = "select count(*) from accession a where a.institute = ?1")
 	Page<Accession> findByInstitute(FaoInstitute institute, Pageable pageable);
 
-	@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")
 	long countByInstitute(FaoInstitute institute);
 
-	@Query(value = "select t.genus, count(a.id) from Accession a inner join a.taxonomy t where a.institute = ?1 group by t.genus order by count(a) desc", countQuery = "select count(distinct a.taxGenus) from Accession a where a.institute = ?1")
+	@Query(value = "select t.genus, count(a.id) from Accession a inner join a.taxonomy t where a.institute = ?1 group by t.genus order by count(a) desc", countQuery = "select count(distinct a.taxonomy.taxGenus) from Accession a where a.institute = ?1")
 	Page<Object[]> statisticsGenusInInstitute(FaoInstitute institute, Pageable pageable);
 
-	@Query(value = "select a.taxSpecies, count(a) from Accession a where a.institute = ?1 group by a.taxSpecies order by count(a) desc", countQuery = "select count(distinct a.taxSpecies) from Accession a where a.institute = ?1")
+	@Query(value = "select t.taxSpecies, count(a) from Accession a inner join a.taxonomy t where a.institute = ?1 group by t.taxSpecies order by count(a) desc", countQuery = "select count(distinct a.taxonomy.taxSpecies) from Accession a where a.institute = ?1")
 	Page<Object[]> statisticsSpeciesInInstitute(FaoInstitute institute, Pageable pageable);
 
 	// FIXME Slow query
@@ -123,8 +117,6 @@ 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);
-
 	@Query("select distinct a.institute from Accession a where a.id in ( ?1 )")
 	List<FaoInstitute> findDistinctInstitutesFor(Set<Long> accessionIds);
 

src/main/java/org/genesys2/server/persistence/domain/TaxonomyRepository.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.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> {
-	Taxonomy getByGenusAndSpecies(String genus, String species);
-
-	List<Taxonomy> findByGenus(String genus);
-
-	Taxonomy getByTaxonName(String fullTaxa);
-
-	@Query("select distinct t.genus from Taxonomy t where t.genus like ?1")
-	List<String> autocompleteGenus(String term, Pageable page);
-
-	@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

@@ -108,12 +108,6 @@ public interface GenesysService {
 	// Page<Object[]> statisticsCropByInstitute(FaoInstitute faoInstitute,
 	// Pageable pageable);
 
-	Page<Accession> listAccessionsByInstituteAndSpecies(FaoInstitute institute, long taxSpecies, Pageable pageable);
-
-	Page<Accession> listAccessionsByTaxGenus(long taxGenusId, Pageable pageable);
-
-	Page<Accession> listAccessionsByTaxSpecies(long taxSpeciesId, Pageable pageable);
-
 	List<Long> listAccessionsIds(Pageable pageable);
 
 	Page<Accession> listAccessionsByCrop(Crop crop, Pageable pageable);

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

@@ -659,8 +659,6 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		if (!ensuredTaxonomy.sameAs(taxonomy)) {
 
 			accession.setTaxonomy(ensuredTaxonomy);
-			accession.setTaxGenus(ensuredTaxonomy.getTaxGenus());
-			accession.setTaxSpecies(ensuredTaxonomy.getTaxSpecies());
 
 			updated = true;
 		}

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

@@ -138,8 +138,11 @@ public class DirectMysqlQuery {
 
 	protected DirectMysqlQuery filter(AppliedFilters filters, MethodResolver methodResolver) {
 		createQuery(whereBuffer, "a.id", filters.get("id"), params);
-		createQuery(whereBuffer, "a.taxGenus", filters.get("genusId"), params);
-		createQuery(whereBuffer, "a.taxSpecies", filters.get("speciesId"), 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, "a.acceNumb", filters.get(FilterConstants.ACCENUMB), params);
 		createQuery(whereBuffer, "a.orgCty", filters.get(FilterConstants.ORGCTY_ISO3), params);
 		createQuery(whereBuffer, "a.instCode", filters.get(FilterConstants.INSTCODE), params);

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

@@ -573,21 +573,6 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		return page;
 	}
 
-	@Override
-	public Page<Accession> listAccessionsByInstituteAndSpecies(FaoInstitute institute, long taxSpecies, Pageable pageable) {
-		return accessionRepository.findByInstituteAndTaxSpecies(institute, taxSpecies, pageable);
-	}
-
-	@Override
-	public Page<Accession> listAccessionsByTaxSpecies(long taxSpecies, Pageable pageable) {
-		return accessionRepository.findByTaxSpecies(taxSpecies, pageable);
-	}
-
-	@Override
-	public Page<Accession> listAccessionsByTaxGenus(long taxGenusId, Pageable pageable) {
-		return accessionRepository.findByTaxGenus(taxGenusId, pageable);
-	}
-
 	@Override
 	public List<Long> listAccessionsIds(Pageable pageable) {
 		return accessionRepository.listAccessionsIds(pageable);

src/test/java/org/genesys2/server/test/BatchRESTServiceTest.java

@@ -240,8 +240,6 @@ public class BatchRESTServiceTest {
 		assertTrue(accession.getTaxonomy() != null);
 		final Taxonomy2 tax = accession.getTaxonomy();
 		System.err.println(tax);
-		System.err.println(accession.getTaxGenus());
-		System.err.println(accession.getTaxSpecies());
 
 		// Modify taxonomy
 		json.put("genus", "Hordeum");
@@ -259,9 +257,6 @@ public class BatchRESTServiceTest {
 		final Taxonomy2 tax2 = accession.getTaxonomy();
 		System.err.println(tax2);
 		assertFalse(tax2.getId().equals(tax.getId()));
-		System.err.println(accession.getTaxGenus());
-		System.err.println(accession.getTaxSpecies());
-		assertFalse(accession.getTaxGenus() == accession.getTaxSpecies());
 
 		// test nothing
 		try {