Historic fixed

src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java

@@ -9,7 +9,6 @@ import java.util.UUID;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
-import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;

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

@@ -20,7 +20,13 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.OrderBy;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
@@ -31,9 +37,22 @@ import javax.persistence.UniqueConstraint;
  *
  */
 @Entity
-@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus",
-		"acceNumb" }) })
+@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus", "acceNumb" }) })
 public class Accession extends AccessionData {
 	public static final List<Accession> EMPTY_LIST = Collections.unmodifiableList(new ArrayList<Accession>());
 
+	@Column(name = "storage", nullable = false)
+	@ElementCollection(fetch = FetchType.LAZY)
+	@CollectionTable(name = "accessionstorage", joinColumns = @JoinColumn(name = "accessionId", referencedColumnName = "id"))
+	@OrderBy("storage")
+	private List<Integer> stoRage = new ArrayList<Integer>();
+
+	public List<Integer> getStoRage() {
+		return stoRage;
+	}
+
+	public void setStoRage(List<Integer> stoRage) {
+		this.stoRage = stoRage;
+	}
+
 }

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

@@ -16,30 +16,65 @@
 
 package org.genesys2.server.model.genesys;
 
+import java.io.Serializable;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Date;
 import java.util.List;
+import java.util.UUID;
 
-import javax.persistence.CollectionTable;
+import javax.persistence.CascadeType;
 import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.FetchType;
+import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.MappedSuperclass;
-import javax.persistence.OrderBy;
+import javax.persistence.MapsId;
+import javax.persistence.OneToOne;
 import javax.persistence.PrePersist;
 import javax.persistence.PreUpdate;
+import javax.persistence.Transient;
+import javax.persistence.Version;
 
+import org.genesys2.server.model.IdUUID;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.springframework.data.annotation.CreatedBy;
+import org.springframework.data.annotation.CreatedDate;
+import org.springframework.data.annotation.LastModifiedBy;
+import org.springframework.data.annotation.LastModifiedDate;
 
 @MappedSuperclass
-public abstract class AccessionData extends AccessionId {
+public abstract class AccessionData implements IdUUID, Serializable {
 
 	public static final List<AccessionData> EMPTY_LIST = Collections.unmodifiableList(new ArrayList<AccessionData>());
 
+	@Id
+	private Long id;
+
+	@Version
+	private long version = 0;
+
+	@CreatedBy
+	private Long createdBy;
+
+	@CreatedDate
+	@Column(name = "createdDate")
+	private Date createdDate;
+
+	@LastModifiedBy
+	private Long lastModifiedBy;
+
+	@LastModifiedDate
+	@Column(name = "lastModifiedDate")
+	private Date lastModifiedDate;
+
+	@MapsId
+	@OneToOne(cascade = { CascadeType.PERSIST, CascadeType.MERGE }, optional = false, orphanRemoval = false)
+	@JoinColumn(name = "id")
+	private AccessionId accessionId;
+
 	@Column(name = "instCode", length = 10, nullable = false)
 	private String instituteCode;
 
@@ -92,12 +127,6 @@ public abstract class AccessionData extends AccessionId {
 	@Column(name = "taxGenus", nullable = false)
 	private long taxGenus;
 
-	@Column(name = "storage", nullable = false)
-	@ElementCollection(fetch = FetchType.LAZY)
-	@CollectionTable(name = "accessionstorage", joinColumns = @JoinColumn(name = "accessionId"))
-	@OrderBy("storage")
-	private List<Integer> stoRage = new ArrayList<Integer>();
-
 	@Column(name = "storage", length = 64, nullable = true)
 	private String storage;
 
@@ -235,13 +264,9 @@ public abstract class AccessionData extends AccessionId {
 		this.taxonomy = taxonomy2;
 	}
 
-	public List<Integer> getStoRage() {
-		return stoRage;
-	}
+	public abstract List<Integer> getStoRage();
 
-	public void setStoRage(List<Integer> stoRage) {
-		this.stoRage = stoRage;
-	}
+	public abstract void setStoRage(List<Integer> stoRage);
 
 	/**
 	 * Returns {@link #getStoRage()} as MCPD string
@@ -258,83 +283,79 @@ public abstract class AccessionData extends AccessionId {
 	protected void setStorage(String storage) {
 		this.storage = storage;
 	}
-	
+
 	public boolean getHistoric() {
 		return historic;
 	}
-	
+
 	public void setHistoric(boolean historic) {
 		this.historic = historic;
 	}
 
+	public long getVersion() {
+		return version;
+	}
+
+	public void setVersion(long version) {
+		this.version = version;
+	}
+
+	public Long getCreatedBy() {
+		return createdBy;
+	}
+
+	public void setCreatedBy(Long createdBy) {
+		this.createdBy = createdBy;
+	}
+
+	public Date getCreatedDate() {
+		return createdDate;
+	}
+
+	public void setCreatedDate(Date createdDate) {
+		this.createdDate = createdDate;
+	}
+
+	public Long getLastModifiedBy() {
+		return lastModifiedBy;
+	}
+
+	public void setLastModifiedBy(Long lastModifiedBy) {
+		this.lastModifiedBy = lastModifiedBy;
+	}
+
+	public Date getLastModifiedDate() {
+		return lastModifiedDate;
+	}
+
+	public void setLastModifiedDate(Date lastModifiedDate) {
+		this.lastModifiedDate = lastModifiedDate;
+	}
+
+	public AccessionId getAccessionId() {
+		return accessionId;
+	}
+
+	public void setAccessionId(AccessionId accessionId) {
+		this.accessionId = accessionId;
+	}
+
+	@Override
+	@Transient
+	public UUID getUuid() {
+		return accessionId.getUuid();
+	}
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
 	@Override
 	public String toString() {
-		return MessageFormat.format("Accession id={0,number,##########} UUID={1}", id, uuid);
-	}
-
-	// public abstract String getAccessionName();
-	//
-	// public abstract String getAcquisitionDate();
-	//
-	// public abstract String getAcquisitionSource();
-	//
-	// public abstract Boolean getAvailability();
-	//
-	// public abstract Boolean getInTrust();
-	//
-	// public abstract Boolean getMlsStatus();
-	//
-	// public abstract FaoInstitute getInstitute();
-	//
-	// public abstract void setInstitute(FaoInstitute institute);
-	//
-	// public abstract String getStorage();
-	//
-	// public abstract List<Integer> getStoRage();
-	//
-	// public abstract String getInstituteCode();
-	//
-	// public abstract void setAccessionName(String accessionName);
-	//
-	// public abstract Taxonomy2 getTaxonomy();
-	//
-	// public abstract void setAcquisitionSource(String acquisitionSource);
-	//
-	// public abstract void setAcquisitionDate(String acquisitionDate);
-	//
-	// public abstract String getOrigin();
-	//
-	// protected abstract void setOrigin(String origin);
-	//
-	// public abstract Country getCountryOfOrigin();
-	//
-	// public abstract void setCountryOfOrigin(Country countryOfOrigin);
-	//
-	// public abstract String getDuplSite();
-	//
-	// public abstract void setDuplSite(String duplSite);
-	//
-	// public abstract Integer getSampleStatus();
-	//
-	// public abstract void setSampleStatus(Integer sampleStatus);
-	//
-	// public abstract Boolean getInSvalbard();
-	//
-	// public abstract void setInSvalbard(Boolean inSvalbard);
-	//
-	// public abstract void setInTrust(Boolean inTrust);
-	//
-	// public abstract void setAvailability(Boolean availability);
-	//
-	// public abstract void setMlsStatus(Boolean mlsStatus);
-	//
-	// public abstract long getTaxGenus();
-	//
-	// protected abstract void setTaxGenus(long taxGenus);
-	//
-	// public abstract void setTaxonomy(Taxonomy2 taxonomy2);
-	//
-	// public abstract void setStoRage(List<Integer> stoRage);
-	//
-	// protected abstract void setStorage(String storage);
+		return MessageFormat.format("Accession id={0,number,##########} UUID={1}", accessionId.getId(), getUuid());
+	}
 }

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

@@ -16,7 +16,16 @@
 
 package org.genesys2.server.model.genesys;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.OrderBy;
 import javax.persistence.Table;
 
 /**
@@ -29,6 +38,12 @@ import javax.persistence.Table;
 @Table(name = "accessionhistoric")
 public class AccessionHistoric extends AccessionData {
 
+	@Column(name = "storage", nullable = false)
+	@ElementCollection(fetch = FetchType.LAZY)
+	@CollectionTable(name = "accessionstorageh", joinColumns = @JoinColumn(name = "accessionId", referencedColumnName = "id"))
+	@OrderBy("storage")
+	private List<Integer> stoRage = new ArrayList<Integer>();
+
 	public AccessionHistoric() {
 
 	}
@@ -37,4 +52,12 @@ public class AccessionHistoric extends AccessionData {
 		SelfCopy.copy(accession, this);
 	}
 
+	public List<Integer> getStoRage() {
+		return stoRage;
+	}
+
+	public void setStoRage(List<Integer> stoRage) {
+		this.stoRage = stoRage;
+	}
+
 }

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

@@ -32,7 +32,7 @@ public class AccessionTrait extends BusinessModel {
 
 	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "accessionId")
-	private Accession accession;
+	private AccessionId accession;
 
 	@Column(name = "metadataId")
 	private long metadataId;
@@ -40,11 +40,11 @@ public class AccessionTrait extends BusinessModel {
 	@Column(name = "methodId")
 	private long methodId;
 
-	public Accession getAccession() {
+	public AccessionId getAccession() {
 		return accession;
 	}
 
-	public void setAccession(Accession accession) {
+	public void setAccession(AccessionId accession) {
 		this.accession = accession;
 	}
 

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

@@ -45,7 +45,7 @@ public class AllAccnames extends BusinessModel {
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
-	private Accession accession;
+	private AccessionId accession;
 
 	@Column(name = "names")
 	@Lob
@@ -68,11 +68,11 @@ public class AllAccnames extends BusinessModel {
 		this.version = version;
 	}
 
-	public Accession getAccession() {
+	public AccessionId getAccession() {
 		return accession;
 	}
 
-	public void setAccession(Accession accession) {
+	public void setAccession(AccessionId accession) {
 		this.accession = accession;
 	}
 

src/main/java/org/genesys2/server/model/json/GenesysJsonFactory.java

@@ -36,7 +36,7 @@ public class GenesysJsonFactory {
 
 		final AccessionJson aj = new AccessionJson();
 		aj.setVersion(accession.getVersion());
-		aj.setGenesysId(accession.getId());
+		aj.setGenesysId(accession.getAccessionId().getId());
 
 		aj.setInstCode(accession.getInstitute().getCode());
 		aj.setAcceNumb(accession.getAccessionName());

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

@@ -31,13 +31,14 @@ public interface AccessionAliasRepository extends JpaRepository<AccessionAlias,
 
 	List<AccessionAlias> findByAccession(AccessionId accession);
 
+	@Query("select aa from AccessionAlias aa where aa.accession = ?1 and aa.aliasType = ?2")
 	List<AccessionAlias> findByAccessionAndAliasType(AccessionId accession, int aliasType);
 
 	@Modifying
 	@Query("delete from AccessionAlias aa where aa.accession.id in ( :ids )")
 	void deleteForAccessions(@Param("ids") Collection<Long> accessionIds);
 
-	@Query("select distinct aa.accession from AccessionAlias aa where aa.usedBy=?1 and aa.name=?2 and aa.aliasType=?3 and aa.accession.institute.code=?1")
+	@Query("select distinct a from Accession a where a.accessionId in (select distinct aa.accession from AccessionAlias aa where aa.usedBy=?1 and aa.name=?2 and aa.aliasType=?3) and a.institute.code=?1")
 	Accession findAccession(String instCode, String name, int aliasType);
 
 	@Query("from AccessionAlias aa where aa.accession.id in ?1")

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

@@ -22,14 +22,15 @@ import java.util.UUID;
 import org.genesys2.server.model.genesys.AccessionHistoric;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
 
 public interface AccessionHistoricRepository extends JpaRepository<AccessionHistoric, Long> {
 
-	AccessionHistoric findOneByUuid(UUID uuid);
-
 	List<AccessionHistoric> findByInstituteAndAccessionName(FaoInstitute faoInstitute, String acceNumb);
 
 	List<AccessionHistoric> findByAccessionName(String acceNumb);
 
+	@Query("select a from AccessionHistoric a where a.accessionId.uuid = ?1")
+	AccessionHistoric findOneByUuid(UUID uuid);
 
 }

src/main/java/org/genesys2/server/persistence/domain/AccessionIdRepository.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 org.genesys2.server.model.genesys.AccessionId;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface AccessionIdRepository extends JpaRepository<AccessionId, Long> {
+
+}

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

@@ -32,4 +32,5 @@ public interface AccessionNameRepository extends JpaRepository<AllAccnames, Long
 	@Query("delete from AllAccnames an where an.accession.id in ?1")
 	void deleteForAccessions(Collection<Long> accessionIds);
 
+
 }

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

@@ -110,6 +110,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query(nativeQuery=true, value="delete from accession where id = ?1")
 	public void deleteActive(long id);
 
+	@Query("select a from Accession a where a.accessionId.uuid = ?1")
 	public Accession findOneByUuid(UUID uuid);
 
 	public List<Accession> findByAccessionName(String acceNumb);

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

@@ -4,6 +4,7 @@ import java.util.List;
 import java.util.UUID;
 
 import org.genesys2.server.model.IdUUID;
+import org.genesys2.server.model.genesys.AccessionData;
 import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.model.impl.FaoInstitute;
 
@@ -11,6 +12,6 @@ public interface ResolverService {
 
 	IdUUID forward(UUID uuid);
 
-	List<AccessionId> findMatches(FaoInstitute faoInstitute, String acceNumb);
+	List<AccessionData> findMatches(FaoInstitute faoInstitute, String acceNumb);
 
 }

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

@@ -23,7 +23,6 @@ import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
-import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
@@ -204,6 +203,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 					LOG.debug("New accession " + dataJson);
 
 				accession = new Accession();
+				accession.setAccessionId(new AccessionId());
 
 				accession.setInstitute(institute);
 				accession.setAccessionName(dataJson.acceNumb);
@@ -218,7 +218,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 					LOG.trace("*** Updating accession " + dataJson);
 			}
 
-			if (accession.getId() == null || useUniqueAcceNumbs && accnJson.get(Api1Constants.Accession.GENUS) != null
+			if (accession.getAccessionId().getId() == null || 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) {
@@ -292,12 +292,12 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 			value = accnJson.get(Api1Constants.Accession.ACCENAME);
 			if (value != null) {
-				acceNames.put(accession, toMcpdArray(accnJson, Api1Constants.Accession.ACCENAME));
+				acceNames.put(accession.getAccessionId(), toMcpdArray(accnJson, Api1Constants.Accession.ACCENAME));
 			}
 
 			value = accnJson.get(Api1Constants.Accession.OTHERNUMB);
 			if (value != null) {
-				otherNumbs.put(accession, toMcpdArray(accnJson, Api1Constants.Accession.OTHERNUMB));
+				otherNumbs.put(accession.getAccessionId(), toMcpdArray(accnJson, Api1Constants.Accession.OTHERNUMB));
 			}
 
 			value = accnJson.get(Api1Constants.Accession.SAMPSTAT);
@@ -323,10 +323,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 			if (accnJson.has(Api1Constants.Accession.COLL)) {
 				final ObjectNode collecting = (ObjectNode) accnJson.get(Api1Constants.Accession.COLL);
-				AccessionCollect accnColl = genesysService.listAccessionCollect(accession);
+				AccessionCollect accnColl = genesysService.listAccessionCollect(accession.getAccessionId());
 				if (accnColl == null) {
 					accnColl = new AccessionCollect();
-					accnColl.setAccession(accession);
+					accnColl.setAccession(accession.getAccessionId());
 				}
 				value = collecting.get(Api1Constants.Collecting.COLLDATE);
 				if (value != null) {
@@ -335,7 +335,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				value = collecting.get(Api1Constants.Collecting.COLLNUMB);
 				if (value != null) {
 					accnColl.setCollNumb(StringUtils.defaultIfBlank(value.textValue(), null));
-					collNumbs.put(accession, toMcpdArray(collecting, Api1Constants.Collecting.COLLNUMB));
+					collNumbs.put(accession.getAccessionId(), toMcpdArray(collecting, Api1Constants.Collecting.COLLNUMB));
 				}
 				value = collecting.get(Api1Constants.Collecting.COLLSRC);
 				if (value != null) {
@@ -374,10 +374,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 			if (accnJson.has(Api1Constants.Accession.GEO)) {
 				final ObjectNode geo = (ObjectNode) accnJson.get(Api1Constants.Accession.GEO);
-				AccessionGeo accnGeo = genesysService.listAccessionGeo(accession);
+				AccessionGeo accnGeo = genesysService.listAccessionGeo(accession.getAccessionId());
 				if (accnGeo == null) {
 					accnGeo = new AccessionGeo();
-					accnGeo.setAccession(accession);
+					accnGeo.setAccession(accession.getAccessionId());
 				}
 				value = geo.get(Api1Constants.Geo.LATITUDE);
 				if (value != null) {
@@ -423,10 +423,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			}
 
 			if (accnJson.has(Api1Constants.Accession.BREDCODE) || accnJson.has(Api1Constants.Accession.ANCEST)) {
-				AccessionBreeding accnBred = genesysService.listAccessionBreeding(accession);
+				AccessionBreeding accnBred = genesysService.listAccessionBreeding(accession.getAccessionId());
 				if (accnBred == null) {
 					accnBred = new AccessionBreeding();
-					accnBred.setAccession(accession);
+					accnBred.setAccession(accession.getAccessionId());
 				}
 				value = accnJson.get(Api1Constants.Accession.BREDCODE);
 				if (value != null) {
@@ -445,10 +445,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 			if (accnJson.has(Api1Constants.Accession.DONORCODE) || accnJson.has(Api1Constants.Accession.DONORNUMB)
 					|| accnJson.has(Api1Constants.Accession.DONORNAME)) {
-				AccessionExchange accnExch = genesysService.listAccessionExchange(accession);
+				AccessionExchange accnExch = genesysService.listAccessionExchange(accession.getAccessionId());
 				if (accnExch == null) {
 					accnExch = new AccessionExchange();