Added AccessionCustomRepository, use Collection<Long> instead of List<Long> in Accession*Repository

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

@@ -40,5 +40,5 @@ public interface AccessionAliasRepository extends JpaRepository<AccessionAlias,
 	Accession findAccession(String instCode, String name, int aliasType);
 
 	@Query("from AccessionAlias aa where aa.accession.id in ?1")
-	List<AccessionAlias> findAllFor(List<Long> accessionIds);
+	List<AccessionAlias> findAllFor(Collection<Long> accessionIds);
 }

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

@@ -34,5 +34,5 @@ public interface AccessionBreedingRepository extends JpaRepository<AccessionBree
 	void deleteForAccessions(Collection<Long> accessionIds);
 
 	@Query("from AccessionBreeding ab where ab.accession.id in ?1")
-	List<AccessionBreeding> findAllFor(List<Long> accessionIds);
+	List<AccessionBreeding> findAllFor(Collection<Long> accessionIds);
 }

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

@@ -34,5 +34,5 @@ public interface AccessionCollectRepository extends JpaRepository<AccessionColle
 	void deleteForAccessions(Collection<Long> accessionIds);
 
 	@Query("from AccessionCollect ac where ac.accession.id in ?1")
-	List<AccessionCollect> findAllFor(List<Long> accessionId);
+	List<AccessionCollect> findAllFor(Collection<Long> accessionIds);
 }

src/main/java/org/genesys2/server/persistence/domain/AccessionCustomRepository.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.Accession;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.impl.NonUniqueAccessionException;
+
+public interface AccessionCustomRepository {
+
+	List<Accession> find(FaoInstitute institute, List<String> acceNumbs, List<String> genera) throws NonUniqueAccessionException;
+
+}

src/main/java/org/genesys2/server/persistence/domain/AccessionCustomRepositoryImpl.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.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+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.impl.FaoInstitute;
+import org.genesys2.server.service.impl.NonUniqueAccessionException;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.stereotype.Repository;
+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);
+
+	@PersistenceContext
+	private EntityManager em;
+
+	private CriteriaBuilder criteriaBuilder;
+
+	@Override
+	public List<Accession> find(FaoInstitute institute, List<String> acceNumbs, List<String> genera) throws NonUniqueAccessionException {
+		boolean uniqueAcceNumbs = institute.hasUniqueAcceNumbs();
+
+		CriteriaQuery<Accession> cq = criteriaBuilder.createQuery(Accession.class);
+		Root<Accession> root = cq.from(Accession.class);
+		cq.select(root);
+		root.fetch("stoRage", JoinType.LEFT);
+		// Join<Accession, Taxonomy2> tax = root.join("taxonomy");
+		List<Predicate> restrictions = new ArrayList<Predicate>();
+
+		if (uniqueAcceNumbs) {
+			restrictions.add(root.get("accessionName").in(acceNumbs));
+			if (LOG.isDebugEnabled())
+				LOG.debug("*** " + 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(root.get("taxonomy.genus"), genera.get(i))));
+			}
+		}
+		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())
+			LOG.debug("*** Loaded accessions " + res.size() + " of " + acceNumbs.size());
+
+		// Check for duplicate names if institute is using unique acceNumbs
+		if (uniqueAcceNumbs) {
+			Set<String> s = new HashSet<String>();
+			for (Accession a : res) {
+				if (s.contains(a.getAccessionName())) {
+					LOG.error("Duplicate accession name instCode=" + a.getInstituteCode() + " acceNumb=" + a.getAccessionName());
+					throw new NonUniqueAccessionException(a.getInstituteCode(), a.getAccessionName());
+				}
+
+				s.add(a.getAccessionName());
+			}
+		}
+
+		return res;
+	}
+
+	@Override
+	public void afterPropertiesSet() throws Exception {
+		this.criteriaBuilder = em.getCriteriaBuilder();
+	}
+}

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

@@ -34,5 +34,5 @@ public interface AccessionExchangeRepository extends JpaRepository<AccessionExch
 	void deleteForAccessions(Collection<Long> accessionIds);
 
 	@Query("from AccessionExchange ae where ae.accession.id in ?1")
-	List<AccessionExchange> findAllFor(List<Long> accessionIds);
+	List<AccessionExchange> findAllFor(Collection<Long> accessionIds);
 }

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

@@ -38,6 +38,6 @@ public interface AccessionGeoRepository extends JpaRepository<AccessionGeo, Long
 	void deleteForAccessions(Collection<Long> accessionIds);
 
 	@Query("from AccessionGeo ag where ag.accession.id in ?1")
-	List<AccessionGeo> findAllFor(List<Long> accessionIds);
+	List<AccessionGeo> findAllFor(Collection<Long> accessionIds);
 
 }

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

@@ -38,5 +38,5 @@ public interface AccessionRemarkRepository extends JpaRepository<AccessionRemark
 	void deleteForAccessions(@Param("ids") Collection<Long> accessionIds);
 
 	@Query("from AccessionRemark ar where ar.accession.id in ?1")
-	List<AccessionRemark> findAllFor(List<Long> accessionIds);
+	List<AccessionRemark> findAllFor(Collection<Long> accessionIds);
 }

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

@@ -62,6 +62,8 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 
 	List<Accession> findByInstituteAndAccessionName(FaoInstitute faoInstitute, String accessionName);
 
+	public List<Accession> findByInstituteAndAccessionName(FaoInstitute institute, List<String> acceNumbs);
+
 	@Query("from Accession a where a.id in ( ?1 )")
 	Page<Accession> findById(Collection<Long> accessionIds, Pageable pageable);
 
@@ -75,6 +77,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query("select a from Accession a where a.taxonomy in ( ?1 )")
 	Page<Accession> findByTaxonomy(Collection<Taxonomy2> taxonomies, Pageable pageable);
 
+	@Query("select a from Accession a where a.institute.code = ?1 and a.accessionName = ?2")
 	Accession findByInstituteCodeAndAccessionName(String instCode, String accessionName);
 
     @Query("select a from Accession a where a.accessionName=?2 and (a.institute.code=?1 or a.institute.codeSGSV=?1) and a.taxonomy.genus=?3")

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

@@ -16,6 +16,8 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.util.Collection;
+import java.util.List;
 import java.util.Set;
 
 import org.genesys2.server.model.genesys.SvalbardData;
@@ -29,4 +31,7 @@ public interface SvalbardRepository extends JpaRepository<SvalbardData, Long> {
 	@Query("delete from SvalbardData sd where sd.id in ?1")
 	void deleteForAccessions(Set<Long> accessionIds);
 
+	@Query("from SvalbardData sd where sd.id in ?1")
+	List<SvalbardData> findAllFor(Collection<Long> accessionIds);
+
 }