Removed referenced 1-to-1 entities from Accession

Introduced AccessionGeo from Environment
Fixed upsert accession REST method

doc/ddl/schema-updates.sql

+
+-- Add @Id, @Version to acq_collect, ...
+
+ALTER TABLE `acq_breeding` CHANGE COLUMN `version` `version` BIGINT NOT NULL DEFAULT 0,
+ CHANGE COLUMN `ALIS_Id` `ALIS_Id` BIGINT NOT NULL  ,
+ ADD COLUMN `id` BIGINT NOT NULL AUTO_INCREMENT  FIRST ,
+ DROP PRIMARY KEY ,
+ ADD PRIMARY KEY (`id`) ,
+ ADD UNIQUE INDEX `ALIS_Id_UNIQUE` (`ALIS_Id` ASC) ;
+
+ALTER TABLE `acq_collect` CHANGE COLUMN `version` `version` BIGINT NOT NULL DEFAULT 0,
+ CHANGE COLUMN `ALIS_Id` `ALIS_Id` BIGINT NOT NULL  ,
+ ADD COLUMN `id` BIGINT NOT NULL AUTO_INCREMENT  FIRST ,
+ DROP PRIMARY KEY ,
+ ADD PRIMARY KEY (`id`) ,
+ ADD UNIQUE INDEX `ALIS_Id_UNIQUE` (`ALIS_Id` ASC) ;
+ 
+ ALTER TABLE `acq_exchange` CHANGE COLUMN `version` `version` BIGINT NOT NULL DEFAULT 0,
+ CHANGE COLUMN `ALIS_Id` `ALIS_Id` BIGINT NOT NULL  ,
+ ADD COLUMN `id` BIGINT NOT NULL AUTO_INCREMENT  FIRST ,
+ DROP PRIMARY KEY ,
+ ADD PRIMARY KEY (`id`) ,
+ ADD UNIQUE INDEX `ALIS_Id_UNIQUE` (`ALIS_Id` ASC) ;
+ 
+ ALTER TABLE `environment` CHANGE COLUMN `version` `version` BIGINT NOT NULL DEFAULT 0,
+ CHANGE COLUMN `ALIS_Id` `ALIS_Id` BIGINT NOT NULL  ,
+ ADD COLUMN `id` BIGINT NOT NULL AUTO_INCREMENT  FIRST ,
+ DROP PRIMARY KEY ,
+ ADD PRIMARY KEY (`id`) ,
+ ADD UNIQUE INDEX `ALIS_Id_UNIQUE` (`ALIS_Id` ASC) ;
+ 
+ ALTER TABLE `accnames` CHANGE COLUMN `version` `version` BIGINT NOT NULL DEFAULT 0,
+ CHANGE COLUMN `ALIS_Id` `ALIS_Id` BIGINT NOT NULL  ,
+ ADD COLUMN `id` BIGINT NOT NULL AUTO_INCREMENT  FIRST ,
+ DROP PRIMARY KEY ,
+ ADD PRIMARY KEY (`id`) ,
+ ADD UNIQUE INDEX `ALIS_Id_UNIQUE` (`ALIS_Id` ASC) ;
+
+
+-- Create acq_geo table
+create table acq_geo as select id, ALIS_Id, version, LatitudeD as lat, LongitudeD as lng, Altitude as alt from environment;
+
+ALTER TABLE `acq_geo` CHANGE COLUMN `id` `id` BIGINT(20) NOT NULL AUTO_INCREMENT, modify column alt double null, ADD PRIMARY KEY (`id`) ;
+
+-- alter table environment drop column LatitudeD, drop column LongitudeD, drop column Altitude;
+
+ALTER TABLE `accession` DROP COLUMN `dataSource` , CHANGE COLUMN `ACC_Numb_HI` `ACC_Numb_HI` VARCHAR(36) NOT NULL COMMENT 'Accession Number at Holding Institute'  , CHANGE COLUMN `Taxon_Code` `Taxon_Code` BIGINT NOT NULL COMMENT 'Taxon Code'  , CHANGE COLUMN `Acquisition_Source` `Acquisition_Source` VARCHAR(3) NULL COMMENT 'Acquisition Source Code'  , CHANGE COLUMN `Acquisition_Date` `Acquisition_Date` VARCHAR(8) NULL COMMENT 'Acquisition Date'  , CHANGE COLUMN `Origin` `Origin` VARCHAR(3) NULL COMMENT 'Country of Origin ISO Code'  , CHANGE COLUMN `Dubl_Inst` `Dubl_Inst` VARCHAR(8) NULL COMMENT 'Duplicate Institute'  , CHANGE COLUMN `Sample_Status` `Sample_Status` VARCHAR(3) NULL COMMENT 'Sample Status Code'  , CHANGE COLUMN `Storage` `Storage` VARCHAR(12) NULL COMMENT 'Storage Type Code'  , CHANGE COLUMN `Genuss` `Genuss` VARCHAR(32) NOT NULL  ;
+

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

@@ -22,10 +22,6 @@ 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.AllAccnames;
-import org.genesys2.server.model.genesys.AllAcqBreeding;
-import org.genesys2.server.model.genesys.AllAcqCollect;
-import org.genesys2.server.model.genesys.AllAcqExchange;
 import org.genesys2.server.model.genesys.Taxonomy;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
@@ -68,31 +64,31 @@ public class AccessionBridge implements FieldBridge {
 			if (institute.getCountry() != null)
 				sd.append(institute.getCountry().getName());
 		}
-		AllAccnames accNames = accession.getAccessionNames();
-		if (accNames != null) {
-			sd.append(accNames.getOtherIds());
-			sd.append(accNames.getAccNames());
-		}
-
-		AllAcqBreeding accBreeding = accession.getAccessionBreeding();
-		if (accBreeding != null) {
-			sd.append(accBreeding.getPedigree());
-			sd.append(accBreeding.getBreederCode());
-		}
-
-		AllAcqCollect accCollect = accession.getAccessionCollection();
-		if (accCollect != null) {
-			sd.append(accCollect.getCollectSite());
-			sd.append(accCollect.getCollectorsNumb());
-			sd.append(accCollect.getCollectingInstitute());
-		}
-
-		AllAcqExchange accExchange = accession.getAccessionExchange();
-		if (accExchange != null) {
-			sd.append(accExchange.getDonorInstitute());
-			sd.append(accExchange.getAccNumbDonor());
-		}
-		
+//		AllAccnames accNames = accession.getAccessionNames();
+//		if (accNames != null) {
+//			sd.append(accNames.getOtherIds());
+//			sd.append(accNames.getAccNames());
+//		}
+//
+//		AllAcqBreeding accBreeding = accession.getAccessionBreeding();
+//		if (accBreeding != null) {
+//			sd.append(accBreeding.getPedigree());
+//			sd.append(accBreeding.getBreederCode());
+//		}
+//
+//		AllAcqCollect accCollect = accession.getAccessionCollection();
+//		if (accCollect != null) {
+//			sd.append(accCollect.getCollectSite());
+//			sd.append(accCollect.getCollectorsNumb());
+//			sd.append(accCollect.getCollectingInstitute());
+//		}
+//
+//		AllAcqExchange accExchange = accession.getAccessionExchange();
+//		if (accExchange != null) {
+//			sd.append(accExchange.getDonorInstitute());
+//			sd.append(accExchange.getAccNumbDonor());
+//		}
+//		
 		LOG.debug("IDX." + name + " = " + sd.toString());
 		Field field = new Field(name, sd.toString(), luceneOptions.getStore(), luceneOptions.getIndex(), luceneOptions.getTermVector());
 		field.setBoost(luceneOptions.getBoost());

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

@@ -20,14 +20,12 @@ package org.genesys2.server.model.genesys;
 
 import java.text.MessageFormat;
 
-import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
-import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 import javax.persistence.Version;
@@ -65,13 +63,6 @@ public class Accession implements java.io.Serializable {
 	private Boolean availability;
 	private Boolean mlsStatus;
 	private String genus;
-	private String dataSource;
-	private AllAccnames accessionNames;
-	private AllAcqBreeding accessionBreeding;
-	private AllAcqCollect accessionCollection;
-	private AllAcqExchange accessionExchange;
-	private AllEnvironment accessionEnvironment;
-	private SvalbardData svalbardData;
 
 	public Accession() {
 	}
@@ -253,70 +244,6 @@ public class Accession implements java.io.Serializable {
 		this.genus = genuss;
 	}
 
-	@OneToOne(optional = true, cascade = { CascadeType.ALL }, mappedBy = "accession")
-	public AllAccnames getAccessionNames() {
-		return accessionNames;
-	}
-
-	public void setAccessionNames(AllAccnames accessionNames) {
-		this.accessionNames = accessionNames;
-	}
-
-	@OneToOne(optional = true, cascade = { CascadeType.ALL }, mappedBy = "accession")
-	public AllAcqBreeding getAccessionBreeding() {
-		return accessionBreeding;
-	}
-
-	public void setAccessionBreeding(AllAcqBreeding accessionBreeding) {
-		this.accessionBreeding = accessionBreeding;
-	}
-
-	@OneToOne(optional = true, cascade = { CascadeType.ALL }, mappedBy = "accession")
-	public AllAcqCollect getAccessionCollection() {
-		return accessionCollection;
-	}
-
-	public void setAccessionCollection(AllAcqCollect accessionCollection) {
-		this.accessionCollection = accessionCollection;
-	}
-
-	@OneToOne(optional = true, cascade = { CascadeType.ALL }, mappedBy = "accession")
-	public AllAcqExchange getAccessionExchange() {
-		return accessionExchange;
-	}
-
-	public void setAccessionExchange(AllAcqExchange accessionExchange) {
-		this.accessionExchange = accessionExchange;
-	}
-
-	@OneToOne(optional = true, cascade = { CascadeType.ALL }, mappedBy = "accession")
-	public AllEnvironment getAccessionEnvironment() {
-		return accessionEnvironment;
-	}
-
-	public void setAccessionEnvironment(AllEnvironment accessionEnvironment) {
-		this.accessionEnvironment = accessionEnvironment;
-	}
-
-	@OneToOne(orphanRemoval = true, cascade = CascadeType.REMOVE, optional = true)
-	@JoinColumn(name = "id", referencedColumnName = "id")
-	public SvalbardData getSvalbardData() {
-		return svalbardData;
-	}
-
-	public void setSvalbardData(SvalbardData svalbardData) {
-		this.svalbardData = svalbardData;
-	}
-
-	@Column(name = "dataSource", length = 45)
-	public String getDataSource() {
-		return dataSource;
-	}
-
-	public void setDataSource(String dataSource) {
-		this.dataSource = dataSource;
-	}
-
 	@Override
 	public String toString() {
 		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, genus, accNumbHi);

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

+/**
+ * Copyright 2013 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 javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+import javax.persistence.Version;
+
+import org.genesys2.server.model.BusinessModel;
+
+@Entity
+@Table(name = "acq_geo")
+public class AccessionGeo extends BusinessModel {
+
+	@Version
+	private long version = 0;
+
+	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
+	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
+	private Accession accession;
+
+	@Column(name = "lng")
+	private Double longitude;
+	@Column(name = "lat")
+	private Double latitude;
+	@Column(name = "alt")
+	private Double altitude;
+
+	public long getVersion() {
+		return version;
+	}
+
+	public void setVersion(long version) {
+		this.version = version;
+	}
+
+	public Accession getAccession() {
+		return accession;
+	}
+
+	public void setAccession(Accession accession) {
+		this.accession = accession;
+	}
+
+	public Double getLongitude() {
+		return this.longitude;
+	}
+
+	public void setLongitude(final Double longitudeD) {
+		this.longitude = longitudeD;
+	}
+
+	public Double getLatitude() {
+		return this.latitude;
+	}
+
+	public void setLatitude(final Double latitudeD) {
+		this.latitude = latitudeD;
+	}
+
+	public Double getAltitude() {
+		return this.altitude;
+	}
+
+	public void setAltitude(final Double altitude) {
+		this.altitude = altitude;
+	}
+
+}

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

@@ -16,35 +16,28 @@
 
 package org.genesys2.server.model.genesys;
 
-// Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
-
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
-import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.Lob;
-import javax.persistence.MapsId;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
+import org.genesys2.server.model.BusinessModel;
+
 /**
  * AllAccnames generated by hbm2java
  */
 @Entity
 @Table(name = "accnames")
-public class AllAccnames {
-
-	@Id
-	@Column(name = "ALIS_Id")
-	private Long id;
+public class AllAccnames extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
-	@MapsId
-	@OneToOne(optional = false, fetch = FetchType.LAZY)
+	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
@@ -59,14 +52,6 @@ public class AllAccnames {
 	public AllAccnames() {
 	}
 
-	public Long getId() {
-		return id;
-	}
-
-	public void setId(Long id) {
-		this.id = id;
-	}
-
 	public long getVersion() {
 		return version;
 	}

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

@@ -16,35 +16,28 @@
 
 package org.genesys2.server.model.genesys;
 
-// Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
-
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
-import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.Lob;
-import javax.persistence.MapsId;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
+import org.genesys2.server.model.BusinessModel;
+
 /**
  * AllAcqBreeding generated by hbm2java
  */
 @Entity
 @Table(name = "acq_breeding")
-public class AllAcqBreeding {
-
-	@Id
-	@Column(name = "ALIS_Id")
-	private Long id;
+public class AllAcqBreeding extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
-	@MapsId
-	@OneToOne(optional = false, fetch = FetchType.LAZY)
+	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
@@ -58,14 +51,6 @@ public class AllAcqBreeding {
 	public AllAcqBreeding() {
 	}
 
-	public Long getId() {
-		return id;
-	}
-
-	public void setId(Long id) {
-		this.id = id;
-	}
-
 	public long getVersion() {
 		return version;
 	}

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

@@ -21,30 +21,25 @@ package org.genesys2.server.model.genesys;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
-import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.Lob;
-import javax.persistence.MapsId;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
+import org.genesys2.server.model.BusinessModel;
+
 /**
  * AllAcqCollect generated by hbm2java
  */
 @Entity
 @Table(name = "acq_collect")
-public class AllAcqCollect {
-
-	@Id
-	@Column(name = "ALIS_Id")
-	private Long id;
+public class AllAcqCollect extends BusinessModel {
 
 	@Version
 	private long version = 0;
-	
-	@MapsId
-	@OneToOne(optional = false, fetch = FetchType.LAZY)
+
+	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
@@ -61,18 +56,9 @@ public class AllAcqCollect {
 	@Lob
 	private String collectSite;
 
-
 	public AllAcqCollect() {
 	}
 
-	public Long getId() {
-		return id;
-	}
-
-	public void setId(Long id) {
-		this.id = id;
-	}
-
 	public long getVersion() {
 		return version;
 	}

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

@@ -16,34 +16,27 @@
 
 package org.genesys2.server.model.genesys;
 
-// Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
-
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
-import javax.persistence.Id;
 import javax.persistence.JoinColumn;
-import javax.persistence.MapsId;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
+import org.genesys2.server.model.BusinessModel;
+
 /**
  * AllAcqExchange generated by hbm2java
  */
 @Entity
 @Table(name = "acq_exchange")
-public class AllAcqExchange {
-
-	@Id
-	@Column(name = "ALIS_Id")
-	private Long id;
+public class AllAcqExchange extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
-	@MapsId
-	@OneToOne(optional = false, fetch = FetchType.LAZY)
+	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 	
@@ -56,16 +49,6 @@ public class AllAcqExchange {
 	public AllAcqExchange() {
 	}
 
-	
-
-	public Long getId() {
-		return id;
-	}
-
-	public void setId(Long id) {
-		this.id = id;
-	}
-
 	public long getVersion() {
 		return version;
 	}

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

@@ -16,31 +16,24 @@
 
 package org.genesys2.server.model.genesys;
 
-// Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
-
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
-import javax.persistence.Id;
 import javax.persistence.JoinColumn;
-import javax.persistence.MapsId;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
+import org.genesys2.server.model.BusinessModel;
+
 @Entity
 @Table(name = "environment")
-public class AllEnvironment {
-
-	@Id
-	@Column(name = "ALIS_Id")
-	private Long id;
+public class AllEnvironment extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
-	@MapsId
-	@OneToOne(optional = false, fetch = FetchType.LAZY)
+	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
@@ -167,14 +160,6 @@ public class AllEnvironment {
 	@Column(name = "Altitude")
 	private Short altitude;
 
-	public Long getId() {
-		return id;
-	}
-
-	public void setId(Long id) {
-		this.id = id;
-	}
-
 	public long getVersion() {
 		return version;
 	}

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

@@ -16,9 +16,12 @@
 
 package org.genesys2.server.persistence.domain;
 
+import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AllAcqBreeding;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface AccessionBreedingRepository extends JpaRepository<AllAcqBreeding, Long> {
 
+	AllAcqBreeding findByAccession(Accession accession);
+
 }