Database model overhaul

src/main/java/org/genesys2/server/model/AuditedModel.java

@@ -19,11 +19,8 @@ package org.genesys2.server.model;
 import java.util.Date;
 
 import javax.persistence.Column;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
 import javax.persistence.MappedSuperclass;
 
-import org.genesys2.server.model.impl.User;
 import org.springframework.data.annotation.CreatedBy;
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.annotation.LastModifiedBy;
@@ -34,28 +31,26 @@ public abstract class AuditedModel extends BusinessModel {
 
 	private static final long serialVersionUID = -5927214471682331909L;
 	@CreatedBy
-	@ManyToOne(optional = true)
-	@JoinColumn(name = "createdBy")
-	private User createdBy;
+	@Column(length = 36)
+	private String createdBy;
 
 	@CreatedDate
 	@Column(name = "createdDate")
 	private Date createdDate;
 
 	@LastModifiedBy
-	@ManyToOne(optional = true)
-	@JoinColumn(name = "lastModifiedBy")
-	private User lastModifiedBy;
+	@Column(length = 36)
+	private String lastModifiedBy;
 
 	@LastModifiedDate
 	@Column(name = "lastModifiedDate")
 	private Date lastModifiedDate;
 
-	public User getCreatedBy() {
+	public String getCreatedBy() {
 		return createdBy;
 	}
 
-	public void setCreatedBy(User createdBy) {
+	public void setCreatedBy(String createdBy) {
 		this.createdBy = createdBy;
 	}
 
@@ -67,11 +62,11 @@ public abstract class AuditedModel extends BusinessModel {
 		this.createdDate = createdDate;
 	}
 
-	public User getLastModifiedBy() {
+	public String getLastModifiedBy() {
 		return lastModifiedBy;
 	}
 
-	public void setLastModifiedBy(User lastModifiedBy) {
+	public void setLastModifiedBy(String lastModifiedBy) {
 		this.lastModifiedBy = lastModifiedBy;
 	}
 

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

@@ -16,79 +16,86 @@
 
 package org.genesys2.server.model.genesys;
 
-// Generated Apr 24, 2013 10:08:59 AM by Hibernate Tools 4.0.0
-
 import java.text.MessageFormat;
 
 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.Table;
 import javax.persistence.UniqueConstraint;
-import javax.persistence.Version;
 
 import org.genesys2.server.lucene.genesys.AccessionBridge;
+import org.genesys2.server.model.VersionedAuditedModel;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.hibernate.search.annotations.ClassBridge;
-import org.hibernate.search.annotations.DocumentId;
 import org.hibernate.search.annotations.Indexed;
 
 @Entity
-// @Table(name = "accession")
-@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(columnNames = { "Institute", "ACC_Numb_HI", "Genuss" }) })
+@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(columnNames = { "instCode", "acceNumb", "genus" }) })
 @Indexed
 @ClassBridge(name = "body", impl = AccessionBridge.class)
-public class Accession implements java.io.Serializable {
+public class Accession extends VersionedAuditedModel {
 	private static final long serialVersionUID = -7630113633534038876L;
-	private Long id;
-	private long version = 0;
+
+	@Column(length = 36)
 	private String uuid;
+	
+	@Column(name = "instCode", length = 6)
 	private String instituteCode;
+
+	@ManyToOne(cascade = {}, optional = true)
+	@JoinColumn(name = "instituteId")
 	private FaoInstitute institute;
-	private String accNumbHi;
+	
+	@Column(name = "acceNumb", nullable = false, length = 128)
+	private String accessionName;
+
+	@ManyToOne(cascade = {}, optional = true)
+	@JoinColumn(name = "taxonomyId")
 	private Taxonomy taxonomy;
+	
+	@Column(name = "acqSrc", length = 3)
 	private String acquisitionSource;
+	
+	@Column(name = "acqDate", length = 8)
 	private String acquisitionDate;
+
+	@Column(name = "orgCty", length = 3)
 	private String origin;
+
+	@ManyToOne(cascade = {}, optional = true)
+	@JoinColumn(name = "orgCtyId", nullable = true)
 	private Country countryOfOrigin;
+
+	@Column(name = "dublInst", length = 8)
 	private String dublInst;
+
+	@Column(name = "sampStat", length = 3)
 	private String sampleStatus;
+
+	@Column(name = "storage", length = 12)
 	private String storage;
+
+	@Column(name = "inSGSV")
 	private Boolean inSvalbard;
+	
+	@Column(name = "inTrust")
 	private Boolean inTrust;
+	
+	@Column(name = "available")
 	private Boolean availability;
+
+	@Column(name = "mlsStat")
 	private Boolean mlsStatus;
+
+	@Column(name = "genus", nullable = false, length = 64)
 	private String genus;
 
 	public Accession() {
 	}
 
-	@Id
-	@GeneratedValue
-	@Column(name = "id", unique = true, nullable = false)
-	@DocumentId
-	public Long getId() {
-		return this.id;
-	}
-
-	public void setId(final Long alisId) {
-		this.id = alisId;
-	}
-
-	@Version
-	public long getVersion() {
-		return version;
-	}
-
-	public void setVersion(long version) {
-		this.version = version;
-	}
-
-	@Column(length = 36)
 	public String getUuid() {
 		return uuid;
 	}
@@ -97,8 +104,6 @@ public class Accession implements java.io.Serializable {
 		this.uuid = uuid;
 	}
 
-	@ManyToOne(cascade = {}, optional = true)
-	@JoinColumn(name = "instituteId")
 	public FaoInstitute getInstitute() {
 		return this.institute;
 	}
@@ -107,7 +112,6 @@ public class Accession implements java.io.Serializable {
 		this.institute = institute;
 	}
 
-	@Column(name = "Institute", length = 6)
 	public String getInstituteCode() {
 		return instituteCode;
 	}
@@ -116,17 +120,14 @@ public class Accession implements java.io.Serializable {
 		this.instituteCode = instituteCode;
 	}
 
-	@Column(name = "ACC_Numb_HI", nullable = false, length = 128)
 	public String getAccessionName() {
-		return this.accNumbHi;
+		return this.accessionName;
 	}
 
-	public void setAccessionName(final String accNumbHi) {
-		this.accNumbHi = accNumbHi;
+	public void setAccessionName(final String accessionName) {
+		this.accessionName = accessionName;
 	}
 
-	@ManyToOne(cascade = {}, optional = true)
-	@JoinColumn(name = "Taxon_Code")
 	public Taxonomy getTaxonomy() {
 		return this.taxonomy;
 	}
@@ -135,7 +136,6 @@ public class Accession implements java.io.Serializable {
 		this.taxonomy = taxonomy;
 	}
 
-	@Column(name = "Acquisition_Source", length = 3)
 	public String getAcquisitionSource() {
 		return this.acquisitionSource;
 	}
@@ -144,7 +144,6 @@ public class Accession implements java.io.Serializable {
 		this.acquisitionSource = acquisitionSource;
 	}
 
-	@Column(name = "Acquisition_Date", length = 8)
 	public String getAcquisitionDate() {
 		return this.acquisitionDate;
 	}
@@ -153,7 +152,6 @@ public class Accession implements java.io.Serializable {
 		this.acquisitionDate = acquisitionDate;
 	}
 
-	@Column(name = "Origin", length = 3)
 	public String getOrigin() {
 		return this.origin;
 	}
@@ -162,8 +160,6 @@ public class Accession implements java.io.Serializable {
 		this.origin = origin;
 	}
 
-	@ManyToOne(cascade = {}, optional = true)
-	@JoinColumn(name = "originId", nullable = true)
 	public Country getCountryOfOrigin() {
 		return countryOfOrigin;
 	}
@@ -172,7 +168,6 @@ public class Accession implements java.io.Serializable {
 		this.countryOfOrigin = countryOfOrigin;
 	}
 
-	@Column(name = "Dubl_Inst", length = 8)
 	public String getDublInst() {
 		return this.dublInst;
 	}
@@ -181,7 +176,6 @@ public class Accession implements java.io.Serializable {
 		this.dublInst = dublInst;
 	}
 
-	@Column(name = "Sample_Status", length = 3)
 	public String getSampleStatus() {
 		return this.sampleStatus;
 	}
@@ -190,7 +184,6 @@ public class Accession implements java.io.Serializable {
 		this.sampleStatus = sampleStatus;
 	}
 
-	@Column(name = "Storage", length = 12)
 	public String getStorage() {
 		return this.storage;
 	}
@@ -199,7 +192,6 @@ public class Accession implements java.io.Serializable {
 		this.storage = storage;
 	}
 
-	@Column(name = "In_Svalbard")
 	public Boolean getInSvalbard() {
 		return this.inSvalbard;
 	}
@@ -208,7 +200,6 @@ public class Accession implements java.io.Serializable {
 		this.inSvalbard = inSvalbard;
 	}
 
-	@Column(name = "In_Trust")
 	public Boolean getInTrust() {
 		return this.inTrust;
 	}
@@ -217,7 +208,6 @@ public class Accession implements java.io.Serializable {
 		this.inTrust = inTrust;
 	}
 
-	@Column(name = "Availability")
 	public Boolean getAvailability() {
 		return this.availability;
 	}
@@ -226,7 +216,6 @@ public class Accession implements java.io.Serializable {
 		this.availability = availability;
 	}
 
-	@Column(name = "MLS_Status")
 	public Boolean getMlsStatus() {
 		return this.mlsStatus;
 	}
@@ -235,7 +224,6 @@ public class Accession implements java.io.Serializable {
 		this.mlsStatus = mlsStatus;
 	}
 
-	@Column(name = "Genuss", nullable = false, length = 64)
 	public String getGenus() {
 		return this.genus;
 	}
@@ -246,6 +234,6 @@ public class Accession implements java.io.Serializable {
 
 	@Override
 	public String toString() {
-		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, genus, accNumbHi);
+		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, genus, accessionName);
 	}
 }

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

@@ -25,23 +25,24 @@ import javax.persistence.Table;
 import javax.persistence.Version;
 
 import org.genesys2.server.model.BusinessModel;
+import org.genesys2.server.model.impl.GeoReferencedEntity;
 
 @Entity
-@Table(name = "acq_geo")
-public class AccessionGeo extends BusinessModel {
+@Table(name = "accessiongeo")
+public class AccessionGeo extends BusinessModel implements GeoReferencedEntity {
 
 	@Version
 	private long version = 0;
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
-	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
+	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
-	@Column(name = "lng")
+	@Column(name = "longitude")
 	private Double longitude;
-	@Column(name = "lat")
+	@Column(name = "latitude")
 	private Double latitude;
-	@Column(name = "alt")
+	@Column(name = "altitude")
 	private Double altitude;
 
 	public long getVersion() {

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

@@ -31,21 +31,21 @@ import org.genesys2.server.model.BusinessModel;
  * AllAccnames generated by hbm2java
  */
 @Entity
-@Table(name = "accnames")
+@Table(name = "accessionname")
 public class AllAccnames extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
-	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
+	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
-	@Column(name = "AccNames")
+	@Column(name = "names")
 	@Lob
 	private String accNames;
 
-	@Column(name = "OtherIds")
+	@Column(name = "otherIds")
 	@Lob
 	private String otherIds;
 

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

@@ -31,20 +31,20 @@ import org.genesys2.server.model.BusinessModel;
  * AllAcqBreeding generated by hbm2java
  */
 @Entity
-@Table(name = "acq_breeding")
+@Table(name = "accessionbreeding")
 public class AllAcqBreeding extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
-	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
+	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
-	@Column(name = "Breeder_Code", length = 8)
+	@Column(name = "breederCode", length = 8)
 	private String breederCode;
 
-	@Column(name = "Pedigree")
+	@Column(name = "pedigree")
 	@Lob
 	private String pedigree;
 

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

@@ -33,26 +33,26 @@ import org.genesys2.server.model.BusinessModel;
  * AllAcqCollect generated by hbm2java
  */
 @Entity
-@Table(name = "acq_collect")
+@Table(name = "accessioncollect")
 public class AllAcqCollect extends BusinessModel {
 
 	@Version
 	private long version = 0;
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
-	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
+	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 
-	@Column(name = "Collect_Date", length = 8)
+	@Column(name = "date", length = 8)
 	private String collectDate;
 
-	@Column(name = "Collectors_Numb", length = 24)
+	@Column(name = "collNumb", length = 24)
 	private String collectorsNumb;
 
-	@Column(name = "Collecting_Institute", length = 8)
+	@Column(name = "instCode", length = 8)
 	private String collectingInstitute;
 
-	@Column(name = "Collect_Site")
+	@Column(name = "site")
 	@Lob
 	private String collectSite;
 

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

@@ -30,20 +30,20 @@ import org.genesys2.server.model.BusinessModel;
  * AllAcqExchange generated by hbm2java
  */
 @Entity
-@Table(name = "acq_exchange")
+@Table(name = "accessionexchange")
 public class AllAcqExchange extends BusinessModel{
 
 	@Version
 	private long version = 0;
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
-	@JoinColumn(name = "ALIS_Id", unique = true, nullable = false, updatable = false)
+	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
 	private Accession accession;
 	
-	@Column(name = "Donor_Institute", length = 8)
+	@Column(name = "donorInst", length = 8)
 	private String donorInstitute;
 	
-	@Column(name = "Acc_Numb_Donor", length = 36)
+	@Column(name = "acceNumb", length = 36)
 	private String accNumbDonor;
 
 	public AllAcqExchange() {

src/main/java/org/genesys2/server/model/genesys/AllEnvironment.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 = "environment")
-public class AllEnvironment 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 = "T_Min_Jan")
-	private Float TMinJan;
-	@Column(name = "T_Min_Feb")
-	private Float TMinFeb;
-	@Column(name = "T_Min_Mar")
-	private Float TMinMar;
-	@Column(name = "T_Min_Apr")
-	private Float TMinApr;
-	@Column(name = "T_Min_May")
-	private Float TMinMay;
-	@Column(name = "T_Min_Jun")
-	private Float TMinJun;
-	@Column(name = "T_Min_Jul")
-	private Float TMinJul;
-	@Column(name = "T_Min_Aug")
-	private Float TMinAug;
-	@Column(name = "T_Min_Sep")
-	private Float TMinSep;
-	@Column(name = "T_Min_Oct")
-	private Float TMinOct;
-	@Column(name = "T_Min_Nov")
-	private Float TMinNov;
-	@Column(name = "T_Min_Dec")
-	private Float TMinDec;
-	@Column(name = "T_Max_Jan")
-	private Float TMaxJan;
-	@Column(name = "T_Max_Feb")
-	private Float TMaxFeb;
-	@Column(name = "T_Max_Mar")
-	private Float TMaxMar;
-	@Column(name = "T_Max_Apr")
-	private Float TMaxApr;
-	@Column(name = "T_Max_May")
-	private Float TMaxMay;
-	@Column(name = "T_Max_Jun")
-	private Float TMaxJun;
-	@Column(name = "T_Max_Jul")
-	private Float TMaxJul;
-	@Column(name = "T_Max_Aug")
-	private Float TMaxAug;
-	@Column(name = "T_Max_Sep")
-	private Float TMaxSep;
-	@Column(name = "T_Max_Oct")
-	private Float TMaxOct;
-	@Column(name = "T_Max_Nov")
-	private Float TMaxNov;
-	@Column(name = "T_Max_Dec")
-	private Float TMaxDec;
-	@Column(name = "P_Jan")
-	private Float PJan;
-	@Column(name = "P_Feb")
-	private Float PFeb;
-	@Column(name = "P_Mar")
-	private Float PMar;
-	@Column(name = "P_Apr")
-	private Float PApr;
-	@Column(name = "P_May")
-	private Float PMay;
-	@Column(name = "P_Jun")
-	private Float PJun;
-	@Column(name = "P_Jul")
-	private Float PJul;
-	@Column(name = "P_Aug")
-	private Float PAug;
-	@Column(name = "P_Sep")
-	private Float PSep;
-	@Column(name = "P_Oct")
-	private Float POct;
-	@Column(name = "P_Nov")
-	private Float PNov;
-	@Column(name = "P_Dec")
-	private Float PDec;
-	@Column(name = "T_Min_Annual")
-	private Float TMinAnnual;
-	@Column(name = "T_Max_Annual")
-	private Float TMaxAnnual;
-	@Column(name = "P_Max_Annual")
-	private Float PMaxAnnual;
-	@Column(name = "Bio_1")
-	private Float bio1;
-	@Column(name = "Bio_2")
-	private Float bio2;
-	@Column(name = "Bio_3")
-	private Float bio3;
-	@Column(name = "Bio_4")
-	private Float bio4;
-	@Column(name = "Bio_5")
-	private Float bio5;