Keep deleted Accessions in AccessionHistoric

TODO.md

+# TODO Historic records #
+
+- Copy /explore to /archive to allow access to historic entries?
+- Use archives to improve resolver service
\ No newline at end of file

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

@@ -12,6 +12,7 @@ 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;
+import org.genesys2.server.model.genesys.AccessionData;
 import org.genesys2.server.model.genesys.AccessionExchange;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionRemark;
@@ -84,7 +85,7 @@ public class AccessionDetails {
 
 	private boolean historic;
 
-	public static AccessionDetails from(Accession accession) {
+	public static AccessionDetails from(AccessionData accession) {
 		AccessionDetails ad = new AccessionDetails();
 		ad.version = accession.getVersion();
 		ad.id = accession.getId();

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

@@ -16,281 +16,24 @@
 
 package org.genesys2.server.model.genesys;
 
-import java.text.MessageFormat;
 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.ManyToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.PrePersist;
-import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
-import org.genesys2.server.model.VersionedAuditedModel;
-import org.genesys2.server.model.impl.Country;
-import org.genesys2.server.model.impl.FaoInstitute;
-import org.genesys2.util.MCPDUtil;
-
+/**
+ * Active accession records with all possible constraints.
+ * 
+ * @author mobreza
+ *
+ */
 @Entity
-@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus", "acceNumb" }) })
-public class Accession extends VersionedAuditedModel {
-	private static final long serialVersionUID = -7630113633534038876L;
-
+@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(length = 36)
-	private String uuid;
-
-	@Column(name = "instCode", length = 10, nullable = false)
-	private String instituteCode;
-
-	@ManyToOne(cascade = {}, optional = false)
-	@JoinColumn(name = "instituteId")
-	private FaoInstitute institute;
-
-	@Column(name = "acceNumb", nullable = false, length = 128)
-	private String accessionName;
-
-	// @Cache(usage=CacheConcurrencyStrategy.READ_WRITE)
-	@ManyToOne(cascade = {}, optional = false)
-	@JoinColumn(name = "taxonomyId2")
-	private Taxonomy2 taxonomy;
-
-	@Column(name = "acqSrc", length = 3)
-	private String acquisitionSource;
-
-	@Column(name = "acqDate", length = 12)
-	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 = "duplSite", length = 64)
-	private String duplSite;
-
-	@Column(name = "sampStat", length = 3)
-	private Integer sampleStatus;
-
-	@Column(name = "inSGSV")
-	private Boolean inSvalbard;
-
-	@Column(name = "inTrust")
-	private Boolean inTrust;
-
-	@Column(name = "available")
-	private Boolean availability;
-
-	@Column(name = "historic", nullable = false)
-	private boolean historic = false;
-
-	@Column(name = "mlsStat")
-	private Boolean mlsStatus;
-
-	@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;
-
-	public Accession() {
-	}
-
-	/**
-	 * Update MCPD {@link #storage}
-	 */
-	@PrePersist
-	@PreUpdate
-	private void prePersist() {
-		if (this.countryOfOrigin != null)
-			this.origin = this.countryOfOrigin.getCode3();
-		else
-			this.origin = null;
-
-		this.taxGenus = getTaxonomy().getTaxGenus();
-		this.instituteCode = getInstitute().getCode();
-		this.storage = MCPDUtil.toMcpdArray(this.stoRage);
-	}
-
-	public String getUuid() {
-		return uuid;
-	}
-
-	public void setUuid(String uuid) {
-		this.uuid = uuid;
-	}
-
-	public FaoInstitute getInstitute() {
-		return this.institute;
-	}
-
-	public void setInstitute(final FaoInstitute institute) {
-		this.institute = institute;
-	}
-
-	public String getInstituteCode() {
-		return instituteCode;
-	}
-
-	protected void setInstituteCode(final String instituteCode) {
-		this.instituteCode = instituteCode;
-	}
-
-	public String getAccessionName() {
-		return this.accessionName;
-	}
-
-	public void setAccessionName(final String accessionName) {
-		this.accessionName = accessionName;
-	}
-
-	public Taxonomy2 getTaxonomy() {
-		return this.taxonomy;
-	}
-
-	public String getAcquisitionSource() {
-		return this.acquisitionSource;
-	}
-
-	public void setAcquisitionSource(final String acquisitionSource) {
-		this.acquisitionSource = acquisitionSource;
-	}
-
-	public String getAcquisitionDate() {
-		return this.acquisitionDate;
-	}
-
-	public void setAcquisitionDate(final String acquisitionDate) {
-		this.acquisitionDate = acquisitionDate;
-	}
-
-	public String getOrigin() {
-		return this.origin;
-	}
-
-	protected void setOrigin(final String origin) {
-		this.origin = origin;
-	}
-
-	public Country getCountryOfOrigin() {
-		return countryOfOrigin;
-	}
-
-	public void setCountryOfOrigin(Country countryOfOrigin) {
-		this.countryOfOrigin = countryOfOrigin;
-	}
-
-	public String getDuplSite() {
-		return this.duplSite;
-	}
-
-	public void setDuplSite(final String duplSite) {
-		this.duplSite = duplSite;
-	}
-
-	public Integer getSampleStatus() {
-		return this.sampleStatus;
-	}
-
-	public void setSampleStatus(final Integer sampleStatus) {
-		this.sampleStatus = sampleStatus;
-	}
-
-	public Boolean getInSvalbard() {
-		return this.inSvalbard;
-	}
-
-	public void setInSvalbard(final Boolean inSvalbard) {
-		this.inSvalbard = inSvalbard;
-	}
-
-	public Boolean getInTrust() {
-		return this.inTrust;
-	}
-
-	public void setInTrust(final Boolean inTrust) {
-		this.inTrust = inTrust;
-	}
-
-	public Boolean getAvailability() {
-		return this.availability;
-	}
-
-	public void setAvailability(final Boolean availability) {
-		this.availability = availability;
-	}
-
-	public Boolean getMlsStatus() {
-		return this.mlsStatus;
-	}
-
-	public void setMlsStatus(final Boolean mlsStatus) {
-		this.mlsStatus = mlsStatus;
-	}
-
-	public long getTaxGenus() {
-		return taxGenus;
-	}
-
-	protected void setTaxGenus(long taxGenus) {
-		this.taxGenus = taxGenus;
-	}
-
-	public void setTaxonomy(Taxonomy2 taxonomy2) {
-		this.taxonomy = taxonomy2;
-	}
-
-	public List<Integer> getStoRage() {
-		return stoRage;
-	}
-
-	public void setStoRage(List<Integer> stoRage) {
-		this.stoRage = stoRage;
-	}
-
-	/**
-	 * Returns {@link #getStoRage()} as MCPD string
-	 * 
-	 * @return MCPD array string
-	 */
-	public String getStorage() {
-		return storage;
-	}
-
-	/**
-	 * Use {@link #setStoRage(List)} instead.
-	 */
-	protected void setStorage(String storage) {
-		this.storage = storage;
-	}
-
-	public void setHistoric(boolean historic) {
-		this.historic = historic;
-	}
-
-	public boolean getHistoric() {
-		return this.historic;
-	}
-
-	@Override
-	public String toString() {
-		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, taxGenus, accessionName);
-	}
 }

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

@@ -71,7 +71,7 @@ public class AccessionAlias extends BusinessModel implements AccessionRelated {
 
 	@ManyToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "accessionId", nullable = false, updatable = false)
-	private Accession accession;
+	private AccessionId accession;
 
 	@Column(name = "name", length = 150)
 	private String name;
@@ -100,11 +100,11 @@ public class AccessionAlias extends BusinessModel implements AccessionRelated {
 	}
 
 	@Override
-	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/AccessionBreeding.java

@@ -46,7 +46,7 @@ public class AccessionBreeding extends BusinessModel implements AccessionRelated
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
-	private Accession accession;
+	private AccessionId accession;
 
 	@Column(name = "breederCode", length = 8)
 	private String breederCode;
@@ -68,11 +68,11 @@ public class AccessionBreeding extends BusinessModel implements AccessionRelated
 	}
 
 	@Override
-	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/AccessionCollect.java

@@ -46,7 +46,7 @@ public class AccessionCollect extends BusinessModel implements AccessionRelated
 
 	@OneToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
 	@JoinColumn(name = "accessionId", unique = true, nullable = false, updatable = false)
-	private Accession accession;
+	private AccessionId accession;
 
 	@Column(name = "collDate", length = 8)
 	private String collDate;
@@ -87,11 +87,11 @@ public class AccessionCollect extends BusinessModel implements AccessionRelated
 	}
 
 	@Override
-	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/AccessionData.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 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.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.MappedSuperclass;
+import javax.persistence.OrderBy;
+import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
+
+import org.genesys2.server.model.impl.Country;
+import org.genesys2.server.model.impl.FaoInstitute;
+
+@MappedSuperclass
+public abstract class AccessionData extends AccessionId {
+
+	public static final List<AccessionData> EMPTY_LIST = Collections.unmodifiableList(new ArrayList<AccessionData>());
+
+	@Column(length = 36)
+	private String uuid;
+
+	public String getUuid() {
+		return uuid;
+	}
+
+	public void setUuid(String uuid) {
+		this.uuid = uuid;
+	}
+
+	@Column(name = "instCode", length = 10, nullable = false)
+	private String instituteCode;
+
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "instituteId")
+	private FaoInstitute institute;
+
+	@Column(name = "acceNumb", nullable = false, length = 128)
+	private String accessionName;
+
+	// @Cache(usage=CacheConcurrencyStrategy.READ_WRITE)
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "taxonomyId2")
+	private Taxonomy2 taxonomy;
+
+	@Column(name = "acqSrc", length = 3)
+	private String acquisitionSource;
+
+	@Column(name = "acqDate", length = 12)
+	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 = "duplSite", length = 64)
+	private String duplSite;
+
+	@Column(name = "sampStat", length = 3)
+	private Integer sampleStatus;
+
+	@Column(name = "inSGSV")
+	private Boolean inSvalbard;
+
+	@Column(name = "inTrust")
+	private Boolean inTrust;
+
+	@Column(name = "available")
+	private Boolean availability;
+
+	@Column(name = "historic", nullable = false)
+	private boolean historic = false;
+
+	@Column(name = "mlsStat")
+	private Boolean mlsStatus;
+
+	@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;
+
+	/**
+	 * Update MCPD {@link #storage}
+	 */
+	@PrePersist
+	@PreUpdate
+	private void prePersist() {
+		if (this.countryOfOrigin != null)
+			this.origin = this.countryOfOrigin.getCode3();
+		else
+			this.origin = null;
+
+		this.instituteCode = getInstitute().getCode();
+	}
+
+	public FaoInstitute getInstitute() {
+		return this.institute;
+	}
+
+	public void setInstitute(final FaoInstitute institute) {
+		this.institute = institute;
+	}
+
+	public String getInstituteCode() {
+		return instituteCode;
+	}
+
+	protected void setInstituteCode(final String instituteCode) {
+		this.instituteCode = instituteCode;
+	}
+
+	public String getAccessionName() {
+		return this.accessionName;
+	}
+
+	public void setAccessionName(final String accessionName) {
+		this.accessionName = accessionName;
+	}
+
+	public Taxonomy2 getTaxonomy() {
+		return this.taxonomy;
+	}
+
+	public String getAcquisitionSource() {
+		return this.acquisitionSource;
+	}
+
+	public void setAcquisitionSource(final String acquisitionSource) {
+		this.acquisitionSource = acquisitionSource;
+	}
+
+	public String getAcquisitionDate() {
+		return this.acquisitionDate;
+	}
+
+	public void setAcquisitionDate(final String acquisitionDate) {
+		this.acquisitionDate = acquisitionDate;
+	}
+
+	public String getOrigin() {
+		return this.origin;
+	}
+
+	protected void setOrigin(final String origin) {
+		this.origin = origin;
+	}
+
+	public Country getCountryOfOrigin() {
+		return countryOfOrigin;
+	}
+
+	public void setCountryOfOrigin(Country countryOfOrigin) {
+		this.countryOfOrigin = countryOfOrigin;
+	}
+
+	public String getDuplSite() {
+		return this.duplSite;
+	}
+
+	public void setDuplSite(final String duplSite) {
+		this.duplSite = duplSite;
+	}
+
+	public Integer getSampleStatus() {
+		return this.sampleStatus;