/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* European Distributed Institute of Taxonomy
* http://www.e-taxonomy.eu
-*
+*
* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
package eu.etaxonomy.cdm.model.taxon;
-import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;
-import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.Index;
-import org.hibernate.annotations.Table;
-
import java.lang.reflect.Method;
-import javax.persistence.*;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+import javax.persistence.Transient;
+import javax.validation.constraints.NotNull;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlIDREF;
-import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.XmlType;
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Index;
+import org.hibernate.annotations.Table;
+import org.hibernate.envers.Audited;
+import org.hibernate.search.annotations.ClassBridge;
+import org.hibernate.search.annotations.ClassBridges;
+import org.hibernate.search.annotations.IndexedEmbedded;
+import org.hibernate.search.annotations.Store;
+
+import eu.etaxonomy.cdm.hibernate.search.AcceptedTaxonBridge;
+import eu.etaxonomy.cdm.hibernate.search.ClassInfoBridge;
+import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
+import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
+import eu.etaxonomy.cdm.validation.Level2;
+import eu.etaxonomy.cdm.validation.Level3;
+import eu.etaxonomy.cdm.validation.annotation.TaxonNameCannotBeAcceptedAndSynonym;
+
/**
- * Upmost abstract class for the use of a taxon name by a reference either
- * as a taxon ("accepted/correct" name) or as a (junior) synonym.
- * For instance: "Juncus longirostris Kuvaev sec. Kirschner, J. et al. 2002".
- * Within a taxonomic view/treatment a taxon name can be used only once.
- *
+ * The upmost (abstract) class for the use of a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} in a {@link eu.etaxonomy.cdm.model.reference.Reference reference}
+ * or within a taxonomic view/treatment either as a {@link Taxon taxon}
+ * ("accepted" respectively "correct" name) or as a (junior) {@link Synonym synonym}.
+ * Within a taxonomic view/treatment or a reference a taxon name can be used
+ * only in one of both described meanings. The reference using the taxon name
+ * is generally cited with "sec." (secundum, sensu). For instance:
+ * "<i>Juncus longirostris</i> Kuvaev sec. Kirschner, J. et al. 2002".
+ * <P>
+ * This class corresponds to: <ul>
+ * <li> TaxonConcept according to the TDWG ontology
+ * <li> TaxonConcept according to the TCS
+ * </ul>
+ *
* @author m.doering
- * @version 1.0
* @created 08-Nov-2007 13:06:56
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "TaxonBase", propOrder = {
"name",
- "sec"
+ "sec",
+ "doubtful",
+ "appendedPhrase",
+ "useNameCache"
})
@Entity
+@Audited
+//@PreFilter("hasPermission(filterObject, 'edit')")
@Table(appliesTo="TaxonBase", indexes = { @Index(name = "taxonBaseTitleCacheIndex", columnNames = { "titleCache" }) })
-public abstract class TaxonBase extends IdentifiableEntity {
-
- static Logger logger = Logger.getLogger(TaxonBase.class);
-
- private static Method methodTaxonNameAddTaxonBase;
-
- private static void initMethods() {
- if (methodTaxonNameAddTaxonBase == null){
- try {
- methodTaxonNameAddTaxonBase = TaxonNameBase.class.getDeclaredMethod("addTaxonBase", TaxonBase.class);
- methodTaxonNameAddTaxonBase.setAccessible(true);
- } catch (Exception e) {
- e.printStackTrace();
- //TODO handle exception
- }
- }
- }
-
- protected TaxonBase(){
- super();
- }
-
- protected TaxonBase(TaxonNameBase taxonNameBase, ReferenceBase sec){
- super();
- if (taxonNameBase != null){
- initMethods();
- this.invokeSetMethod(methodTaxonNameAddTaxonBase, taxonNameBase);
- }
- this.setSec(sec);
- }
-
- //The assignment to the Taxon or to the Synonym class is not definitive
+@TaxonNameCannotBeAcceptedAndSynonym(groups = Level3.class)
+@ClassBridges({
+ @ClassBridge(name="classInfo",
+ index = org.hibernate.search.annotations.Index.YES,
+ store = Store.YES,
+ impl = ClassInfoBridge.class),
+ @ClassBridge(name="accTaxon", // TODO rename to acceptedTaxon, since we are usually not using abbreviations for field names
+ index = org.hibernate.search.annotations.Index.YES,
+ store = Store.YES,
+ impl = AcceptedTaxonBridge.class),
+ @ClassBridge(impl = eu.etaxonomy.cdm.hibernate.search.NomenclaturalSortOrderBrigde.class)
+})
+public abstract class TaxonBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> implements Cloneable {
+ private static final long serialVersionUID = -3589185949928938529L;
+ private static final Logger logger = Logger.getLogger(TaxonBase.class);
+
+ private static Method methodTaxonNameAddTaxonBase;
+
+ static {
+ try {
+ methodTaxonNameAddTaxonBase = TaxonNameBase.class.getDeclaredMethod("addTaxonBase", TaxonBase.class);
+ methodTaxonNameAddTaxonBase.setAccessible(true);
+ } catch (Exception e) {
+ logger.error(e);
+ for(StackTraceElement ste : e.getStackTrace()) {
+ logger.error(ste);
+ }
+ }
+ }
+
+ //The assignment to the Taxon or to the Synonym class is not definitive
@XmlAttribute(name = "isDoubtful")
- private boolean isDoubtful;
-
+ private boolean doubtful;
+
+
@XmlElement(name = "Name", required = true)
@XmlIDREF
@XmlSchemaType(name = "IDREF")
- private TaxonNameBase name;
-
- // The concept reference
+ @ManyToOne(fetch = FetchType.LAZY)
+ @IndexedEmbedded
+ @Cascade(CascadeType.SAVE_UPDATE)
+ @NotNull(groups = Level2.class)
+ private TaxonNameBase<?,?> name;
+
+ // The concept reference
@XmlElement(name = "Sec")
@XmlIDREF
@XmlSchemaType(name = "IDREF")
- private ReferenceBase sec;
-
- @Override
- public String generateTitle() {
- String title;
- if (name != null && name.getTitleCache() != null){
- title = name.getTitleCache() + " sec. ";
- if (sec != null){
- title += sec.getTitleCache();
- }else{
- title += "???";
- }
- }else{
- title = this.toString();
- }
- return title;
- }
-
- @ManyToOne
- @JoinColumn(name="taxonName_fk")
- @Cascade(CascadeType.SAVE_UPDATE)
- public TaxonNameBase getName(){
- return this.name;
- }
- @Deprecated //for hibernate use only, use taxon.addDescription() instead
- private void setName(TaxonNameBase newName){
- this.name = newName;
- }
-
- @Transient
- public HomotypicalGroup getHomotypicGroup(){
- if (this.getName() == null){
- return null;
- }else{
- return this.getName().getHomotypicalGroup();
- }
- }
-
- public boolean isDoubtful(){
- return this.isDoubtful;
- }
- public void setDoubtful(boolean isDoubtful){
- this.isDoubtful = isDoubtful;
- }
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- public ReferenceBase getSec() {
- return sec;
- }
-
- public void setSec(ReferenceBase sec) {
- this.sec = sec;
- }
-
- @Transient
- public boolean isSaveable(){
- if ( (this.getName() == null) || (this.getSec() == null) ){
- return false;
- }else{
- this.toString();
- return true;
- }
- }
-
+ @ManyToOne(fetch = FetchType.LAZY)
+ @Cascade(CascadeType.SAVE_UPDATE)
+ @NotNull(groups = Level2.class)
+ @IndexedEmbedded
+ private Reference<?> sec;
+
+
+ @XmlElement(name = "AppendedPhrase")
+ private String appendedPhrase;
+
+ @XmlAttribute(name= "UseNameCache")
+ private boolean useNameCache = false;
+
+
+// ************* CONSTRUCTORS *************/
+ /**
+ * Class constructor: creates a new empty (abstract) taxon.
+ *
+ * @see #TaxonBase(TaxonNameBase, Reference)
+ */
+ protected TaxonBase(){
+ super();
+ }
+
+ /**
+ * Class constructor: creates a new (abstract) taxon with the
+ * {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}
+ * using it.
+ *
+ * @param taxonNameBase the taxon name used
+ * @param sec the reference using the taxon name
+ * @see #TaxonBase()
+ */
+ protected TaxonBase(TaxonNameBase taxonNameBase, Reference sec){
+ super();
+ if (taxonNameBase != null){
+ this.invokeSetMethod(methodTaxonNameAddTaxonBase, taxonNameBase);
+ }
+ this.setSec(sec);
+ }
+
+//********* METHODS **************************************/
+
+ /**
+ * Generates and returns the string with the full scientific name (including
+ * authorship) of the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used in <i>this</i>
+ * (abstract) taxon as well as the title of the {@link eu.etaxonomy.cdm.model.reference.Reference reference} using
+ * this taxon name. This string may be stored in the inherited
+ * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
+ * This method overrides the generic and inherited generateTitle() method
+ * from {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity IdentifiableEntity}.
+ *
+ * @return the string with the full scientific name of the taxon name
+ * and with the title of the reference involved in <i>this</i> (abstract) taxon
+ * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
+ * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
+ */
+// @Override
+// public String generateTitle() {
+// String title;
+// if (name != null && name.getTitleCache() != null){
+// title = name.getTitleCache() + " sec. ";
+// if (sec != null){
+// title += sec.getTitleCache();
+// }else{
+// title += "???";
+// }
+// }else{
+// title = this.toString();
+// }
+// return title;
+// }
+
+ /**
+ * Returns the {@link TaxonNameBase taxon name} used in <i>this</i> (abstract) taxon.
+ */
+ public TaxonNameBase getName(){
+ return this.name;
+ }
+
+ /*
+ * @see #getName
+ */
+ public void setName(TaxonNameBase name) {
+ if (this.name != null){
+ this.name.getTaxonBases().remove(this);
+ }
+ if(name != null) {
+ name.getTaxonBases().add(this);
+ }
+ this.name = name;
+ }
+
+ /**
+ * Returns the {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical group} of the
+ * {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used in <i>this</i> (abstract) taxon.
+ */
+ @Transient
+ public HomotypicalGroup getHomotypicGroup(){
+ if (this.getName() == null){
+ return null;
+ }else{
+ return this.getName().getHomotypicalGroup();
+ }
+ }
+
+ /**
+ * Returns the boolean value indicating whether the assignment of <i>this</i>
+ * (abstract) taxon to the {@link Taxon Taxon} or to the {@link Synonym Synonym} class
+ * is definitive (false) or not (true). If this flag is set the use of <i>this</i> (abstract)
+ * taxon as an "accepted/correct" name or as a (junior) "synonym" might
+ * still change in the course of taxonomical working process.
+ */
+ public boolean isDoubtful(){
+ return this.doubtful;
+ }
+ /**
+ * @see #isDoubtful()
+ */
+ public void setDoubtful(boolean doubtful){
+ this.doubtful = doubtful;
+ }
+
+ /**
+ * Returns the {@link eu.etaxonomy.cdm.model.reference.Reference reference} of <i>this</i> (abstract) taxon.
+ * This is the reference or the treatment using the {@link TaxonNameBase taxon name}
+ * in <i>this</i> (abstract) taxon.
+ */
+ public Reference getSec() {
+ return sec;
+ }
+
+ /**
+ * @see #getSec()
+ */
+ public void setSec(Reference sec) {
+ this.sec = sec;
+ }
+
+
+
+ /**
+ * An appended phrase is a phrase that is added to the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name}
+ * 's title cache to be used just in this taxon. E.g. the phrase "sensu latu" may be added
+ * to the name to describe this taxon more precisely.
+ * If {@link #isUseNameCache()}
+ * @return the appendedPhrase
+ */
+ public String getAppendedPhrase() {
+ return appendedPhrase;
+ }
+
+ /**
+ * @param appendedPhrase the appendedPhrase to set
+ */
+ public void setAppendedPhrase(String appendedPhrase) {
+ this.appendedPhrase = appendedPhrase;
+ }
+
+ /**
+ * @return the useNameCache
+ */
+ public boolean isUseNameCache() {
+ return useNameCache;
+ }
+
+ /**
+ * @param useNameCache the useNameCache to set
+ */
+ public void setUseNameCache(boolean useNameCache) {
+ this.useNameCache = useNameCache;
+ }
+
+ @Transient
+ public abstract boolean isOrphaned();
+//*********************** CLONE ********************************************************/
+
+ /**
+ * Clones <i>this</i> taxon. This is a shortcut that enables to create
+ * a new instance with empty taxon name and sec reference.
+ *
+ * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
+ * @see java.lang.Object#clone()
+ */
+ @Override
+ public Object clone() {
+ TaxonBase result;
+ try {
+ result = (TaxonBase)super.clone();
+ result.setSec(null);
+
+ return result;
+ } catch (CloneNotSupportedException e) {
+ logger.warn("Object does not implement cloneable");
+ e.printStackTrace();
+ return null;
+ }
+
+
+ }
+
}
\ No newline at end of file
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