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Commit 98cfb73b authored by Matija Obreza's avatar Matija Obreza
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Keep deleted Accessions in AccessionHistoric

parent a62674ea
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TODO.md 0 → 100644
View file @ 98cfb73b
# 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
View file @ 98cfb73b
......@@ -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
View file @ 98cfb73b
......@@ -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
View file @ 98cfb73b
......@@ -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
View file @ 98cfb73b
......@@ -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
View file @ 98cfb73b
......@@ -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 0 → 100644
View file @ 98cfb73b
/**
* 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;
}
public void setSampleStatus(final Integer sampleStatus) {
this.sampleStatus = sampleStatus;
}
public Boolean getInSvalbard() {
return this.inSvalbard;