package eu.etaxonomy.cdm.model.common;
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.Index;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import javax.persistence.Column;
+import javax.persistence.Embedded;
+import javax.persistence.FetchType;
+import javax.persistence.MappedSuperclass;
+import javax.persistence.OneToMany;
+import javax.persistence.Transient;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-import eu.etaxonomy.cdm.model.media.IdentifyableMediaEntity;
-import eu.etaxonomy.cdm.model.media.Media;
-import eu.etaxonomy.cdm.model.media.Rights;
-
-
-import java.util.HashSet;
-import java.util.Set;
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.IndexColumn;
+import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.FieldBridge;
+import org.hibernate.search.annotations.Fields;
-import javax.persistence.*;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
+import eu.etaxonomy.cdm.hibernate.StripHtmlBridge;
+import eu.etaxonomy.cdm.jaxb.FormattedTextAdapter;
+import eu.etaxonomy.cdm.jaxb.LSIDAdapter;
+import eu.etaxonomy.cdm.model.media.Rights;
+import eu.etaxonomy.cdm.model.name.NonViralName;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
/**
* Superclass for the primary CDM classes that can be referenced from outside via LSIDs and contain a simple generated title string as a label for human reading.
"protectedTitleCache",
"rights",
"extensions",
+ "credits",
"sources"
})
@MappedSuperclass
-public abstract class IdentifiableEntity<T extends IdentifiableEntity> extends AnnotatableEntity<T> implements IOriginalSource, IIdentifiableEntitiy<T> {
- static Logger logger = Logger.getLogger(IdentifiableEntity.class);
+public abstract class IdentifiableEntity<S extends IIdentifiableEntityCacheStrategy> extends AnnotatableEntity
+implements ISourceable, IIdentifiableEntity, Comparable<IdentifiableEntity> {
+ private static final long serialVersionUID = -5610995424730659058L;
+ private static final Logger logger = Logger.getLogger(IdentifiableEntity.class);
@XmlTransient
- public final boolean PROTECTED = true;
+ public static final boolean PROTECTED = true;
@XmlTransient
- public final boolean NOT_PROTECTED = false;
+ public static final boolean NOT_PROTECTED = false;
- @XmlElement(name = "LSID")
- private String lsid;
+ @XmlElement(name = "LSID", type = String.class)
+ @XmlJavaTypeAdapter(LSIDAdapter.class)
+ @Embedded
+ private LSID lsid;
@XmlElement(name = "TitleCache", required = true)
+ @XmlJavaTypeAdapter(FormattedTextAdapter.class)
+ @Column(length=255, name="titleCache")
+ @Fields({@Field(index = org.hibernate.search.annotations.Index.TOKENIZED),
+ @Field(name = "titleCache_forSort", index = org.hibernate.search.annotations.Index.UN_TOKENIZED)
+ })
+ @FieldBridge(impl=StripHtmlBridge.class)
private String titleCache;
//if true titleCache will not be automatically generated/updated
@XmlElementWrapper(name = "Rights")
@XmlElement(name = "Rights")
- private Set<Rights> rights = getNewRightsSet();
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ private Set<Rights> rights = new HashSet<Rights>();
+
+ @XmlElementWrapper(name = "Credits")
+ @XmlElement(name = "Credit")
+ @IndexColumn(name="sortIndex", base = 0)
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ private List<Credit> credits = new ArrayList<Credit>();
@XmlElementWrapper(name = "Extensions")
@XmlElement(name = "Extension")
- private Set<Extension> extensions = getNewExtensionSet();
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ private Set<Extension> extensions = new HashSet<Extension>();
@XmlElementWrapper(name = "Sources")
@XmlElement(name = "OriginalSource")
- private Set<OriginalSource> sources = getNewOriginalSourcesSet();
-
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ private Set<OriginalSource> sources = new HashSet<OriginalSource>();
+
+ @XmlTransient
+ @Transient
+ protected S cacheStrategy;
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#getLsid()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getLsid()
*/
- public String getLsid(){
+ public LSID getLsid(){
return this.lsid;
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#setLsid(java.lang.String)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#setLsid(java.lang.String)
*/
- public void setLsid(String lsid){
+ public void setLsid(LSID lsid){
this.lsid = lsid;
}
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#generateTitle()
+ /**
+ * By default, we expect most cdm objects to be abstract things
+ * i.e. unable to return a data representation.
+ *
+ * Specific subclasses (e.g. Sequence) can override if necessary.
*/
- public abstract String generateTitle();
+ public byte[] getData() {
+ return null;
+ }
- //@Index(name="titleCacheIndex")
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#getTitleCache()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getTitleCache()
*/
+ //@Transient
public String getTitleCache(){
if (protectedTitleCache){
return this.titleCache;
}
// is title dirty, i.e. equal NULL?
if (titleCache == null){
- this.titleCache = generateTitle();
+ this.setTitleCache(generateTitle(),protectedTitleCache) ; //for truncating
}
return titleCache;
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#setTitleCache(java.lang.String)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#setTitleCache(java.lang.String)
*/
public void setTitleCache(String titleCache){
- //TODO truncation of title cach
- if (titleCache != null && titleCache.length() > 254){
- logger.warn("Truncation of title cache: " + this.toString());
- titleCache = titleCache.substring(0, 252) + "...";
- }
- this.titleCache = titleCache;
- this.setProtectedTitleCache(PROTECTED);
+ setTitleCache(titleCache, PROTECTED);
}
+
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#setTitleCache(java.lang.String, boolean)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#setTitleCache(java.lang.String, boolean)
*/
public void setTitleCache(String titleCache, boolean protectCache){
+ //TODO truncation of title cache
+ if (titleCache != null && titleCache.length() > 254){
+ logger.warn("Truncation of title cache: " + this.toString() + "/" + titleCache);
+ titleCache = titleCache.substring(0, 251) + "...";
+ }
this.titleCache = titleCache;
this.setProtectedTitleCache(protectCache);
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#getRights()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getRights()
*/
- @ManyToMany
- @Cascade({CascadeType.SAVE_UPDATE})
- public Set<Rights> getRights(){
- return this.rights;
- }
-
- protected void setRights(Set<Rights> rights) {
- this.rights = rights;
+ public Set<Rights> getRights() {
+ return this.rights;
}
+
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#addRights(eu.etaxonomy.cdm.model.media.Rights)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#addRights(eu.etaxonomy.cdm.model.media.Rights)
*/
public void addRights(Rights right){
this.rights.add(right);
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#removeRights(eu.etaxonomy.cdm.model.media.Rights)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#removeRights(eu.etaxonomy.cdm.model.media.Rights)
*/
public void removeRights(Rights right){
this.rights.remove(right);
}
+
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#getExtensions()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getCredits()
+ */
+ public List<Credit> getCredits() {
+ return this.credits;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getCredits(int)
+ */
+ public Credit getCredits(int index){
+ return this.credits.get(index);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#addCredit(eu.etaxonomy.cdm.model.common.Credit)
+ */
+ public void addCredit(Credit credit){
+ this.credits.add(credit);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#addCredit(eu.etaxonomy.cdm.model.common.Credit, int)
+ */
+ public void addCredit(Credit credit, int index){
+ this.credits.add(index, credit);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#removeCredit(eu.etaxonomy.cdm.model.common.Credit)
+ */
+ public void removeCredit(Credit credit){
+ this.credits.remove(credit);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#removeCredit(int)
+ */
+ public void removeCredit(int index){
+ this.credits.remove(index);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getExtensions()
*/
- @OneToMany//(mappedBy="extendedObj")
- @Cascade({CascadeType.SAVE_UPDATE})
public Set<Extension> getExtensions(){
return this.extensions;
}
- protected void setExtensions(Set<Extension> extensions) {
- this.extensions = extensions;
+
+ public void addExtension(String value, ExtensionType extensionType){
+ Extension.NewInstance(this, value, extensionType);
}
+
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#addExtension(eu.etaxonomy.cdm.model.common.Extension)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#addExtension(eu.etaxonomy.cdm.model.common.Extension)
*/
public void addExtension(Extension extension){
- this.extensions.add(extension);
+ if (extension != null){
+ extension.setExtendedObj(this);
+ this.extensions.add(extension);
+ }
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#removeExtension(eu.etaxonomy.cdm.model.common.Extension)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#removeExtension(eu.etaxonomy.cdm.model.common.Extension)
*/
public void removeExtension(Extension extension){
- this.extensions.remove(extension);
+ if (extension != null){
+ extension.setExtendedObj(null);
+ this.extensions.remove(extension);
+ }
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#isProtectedTitleCache()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#isProtectedTitleCache()
*/
public boolean isProtectedTitleCache() {
return protectedTitleCache;
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#setProtectedTitleCache(boolean)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#setProtectedTitleCache(boolean)
*/
public void setProtectedTitleCache(boolean protectedTitleCache) {
this.protectedTitleCache = protectedTitleCache;
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#getSources()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getSources()
*/
- @OneToMany //(mappedBy="sourcedObj")
- @Cascade({CascadeType.SAVE_UPDATE})
public Set<OriginalSource> getSources() {
return this.sources;
}
- protected void setSources(Set<OriginalSource> sources) {
- this.sources = sources;
- }
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#addSource(eu.etaxonomy.cdm.model.common.OriginalSource)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#addSource(eu.etaxonomy.cdm.model.common.OriginalSource)
*/
public void addSource(OriginalSource source) {
if (source != null){
}
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#removeSource(eu.etaxonomy.cdm.model.common.OriginalSource)
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#removeSource(eu.etaxonomy.cdm.model.common.OriginalSource)
*/
public void removeSource(OriginalSource source) {
this.sources.remove(source);
}
/* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy#toString()
+ * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#toString()
*/
@Override
public String toString() {
return result;
}
+ public int compareTo(IdentifiableEntity identifiableEntity) {
+
+ int result = 0;
+
+ if (identifiableEntity == null) {
+ throw new NullPointerException("Cannot compare to null.");
+ }
+
+ // First, compare the name cache.
+ // TODO: Avoid using instanceof operator
+ // Use Class.getDeclaredMethod() instead to find out whether class has getNameCache() method?
+
+ String specifiedNameCache = "";
+ String thisNameCache = "";
+ String specifiedTitleCache = "";
+ String thisTitleCache = "";
+ String specifiedReferenceTitleCache = "";
+ String thisReferenceTitleCache = "";
+
+ if(identifiableEntity instanceof NonViralName) {
+ specifiedNameCache = HibernateProxyHelper.deproxy(identifiableEntity, NonViralName.class).getNameCache();
+ specifiedTitleCache = identifiableEntity.getTitleCache();
+
+ } else if(identifiableEntity instanceof TaxonBase) {
+ TaxonBase taxonBase = HibernateProxyHelper.deproxy(identifiableEntity, TaxonBase.class);
+
+ TaxonNameBase<?,?> taxonNameBase = taxonBase.getName();
+ specifiedNameCache = HibernateProxyHelper.deproxy(taxonNameBase, NonViralName.class).getNameCache();
+ specifiedTitleCache = taxonNameBase.getTitleCache();
+
+ //specifiedReferenceTitleCache = ((TaxonBase)identifiableEntity).getSec().getTitleCache();
+// ReferenceBase referenceBase = taxonBase.getSec();
+// if (referenceBase != null) {
+// FIXME: HibernateProxyHelper.deproxy(referenceBase, ReferenceBase.class) throws exception
+// referenceBase = HibernateProxyHelper.deproxy(referenceBase, ReferenceBase.class);
+// specifiedReferenceTitleCache = referenceBase.getTitleCache();
+// }
+ }
+
+ if(this instanceof NonViralName) {
+ thisNameCache = HibernateProxyHelper.deproxy(this, NonViralName.class).getNameCache();
+ thisTitleCache = getTitleCache();
+ } else if(this instanceof TaxonBase) {
+ TaxonNameBase<?,?> taxonNameBase= HibernateProxyHelper.deproxy(this, TaxonBase.class).getName();
+ thisNameCache = HibernateProxyHelper.deproxy(taxonNameBase, NonViralName.class).getNameCache();
+ thisTitleCache = taxonNameBase.getTitleCache();
+ thisReferenceTitleCache = getTitleCache();
+ }
+
+ // Compare name cache of taxon names
+
+ if (!specifiedNameCache.equals("") && !thisNameCache.equals("")) {
+ result = thisNameCache.compareTo(specifiedNameCache);
+ }
+
+ // Compare title cache of taxon names
+
+ if ((result == 0) && (!specifiedTitleCache.equals("") || !thisTitleCache.equals(""))) {
+ result = thisTitleCache.compareTo(specifiedTitleCache);
+ }
+
+ // Compare title cache of taxon references
+
+ if ((result == 0) && (!specifiedReferenceTitleCache.equals("") || !thisReferenceTitleCache.equals(""))) {
+ result = thisReferenceTitleCache.compareTo(specifiedReferenceTitleCache);
+ }
+
+ return result;
+ }
+
+
//****************** CLONE ************************************************/
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.common.AnnotatableEntity#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
IdentifiableEntity result = (IdentifiableEntity)super.clone();
//Extensions
- Set<Extension> newExtensions = getNewExtensionSet();
+ result.extensions = new HashSet<Extension>();
for (Extension extension : this.extensions ){
- Extension newExtension = (Extension)extension.clone(this);
- newExtensions.add(newExtension);
+ Extension newExtension = (Extension)extension.clone();
+ result.addExtension(newExtension);
}
- result.setExtensions(newExtensions);
//OriginalSources
- Set<OriginalSource> newOriginalSources = getNewOriginalSourcesSet();
+ result.sources = new HashSet<OriginalSource>();
for (OriginalSource originalSource : this.sources){
- OriginalSource newSource = (OriginalSource)originalSource.clone(this);
- newOriginalSources.add(newSource);
+ OriginalSource newSource = (OriginalSource)originalSource.clone();
+ result.addSource(newSource);
}
- result.setSources(newOriginalSources);
//Rights
- Set<Rights> rights = getNewRightsSet();
- rights.addAll(this.rights);
- result.setRights(rights);
+ result.rights = new HashSet<Rights>();
+ for(Rights rights : this.rights) {
+ result.addRights(rights);
+ }
//result.setLsid(lsid);
//result.setTitleCache(titleCache);
//result.setProtectedTitleCache(protectedTitleCache); //must be after setTitleCache
//no changes to: lsid, titleCache, protectedTitleCache
+
+ //empty titleCache
+ if (! protectedTitleCache){
+ titleCache = null;
+ }
return result;
}
- @Transient
- private Set<Extension> getNewExtensionSet(){
- return new HashSet<Extension>();
+ /**
+ * Returns the {@link eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy cache strategy} used to generate
+ * several strings corresponding to <i>this</i> identifiable entity
+ * (in particular taxon name caches and author strings).
+ *
+ * @return the cache strategy used for <i>this</i> identifiable entity
+ * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
+ */
+ public S getCacheStrategy() {
+ return this.cacheStrategy;
}
+ /**
+ * @see #getCacheStrategy()
+ */
- @Transient
- private Set<OriginalSource> getNewOriginalSourcesSet(){
- return new HashSet<OriginalSource>();
+ public void setCacheStrategy(S cacheStrategy) {
+ this.cacheStrategy = cacheStrategy;
}
- @Transient
- private Set<Rights> getNewRightsSet(){
- return new HashSet<Rights>();
+ public String generateTitle() {
+ if (cacheStrategy == null){
+ logger.warn("No CacheStrategy defined for "+ this.getClass() + ": " + this.getUuid());
+ return null;
+ }else{
+ return cacheStrategy.getTitleCache(this);
+ }
}
-
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff