package eu.etaxonomy.cdm.model.occurrence;
-import eu.etaxonomy.cdm.model.common.IdentifyableMediaEntity;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Transient;
+import javax.validation.constraints.Min;
+import javax.validation.constraints.NotNull;
+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.XmlIDREF;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+
+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.Field;
+import org.hibernate.search.annotations.IndexedEmbedded;
+
+import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.LanguageString;
-import eu.etaxonomy.cdm.model.common.MultilanguageSet;
import eu.etaxonomy.cdm.model.description.DescriptionBase;
import eu.etaxonomy.cdm.model.description.Sex;
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
import eu.etaxonomy.cdm.model.description.Stage;
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import java.util.*;
-import javax.persistence.*;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
+import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
+import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
/**
* type figures are observations with at least a figure object in media
* @version 1.0
* @created 08-Nov-2007 13:06:41
*/
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "SpecimenOrObservationBase", propOrder = {
+ "sex",
+ "individualCount",
+ "lifeStage",
+ "description",
+ "descriptions",
+ "determinations",
+ "derivationEvents"
+})
+@XmlRootElement(name = "SpecimenOrObservationBase")
@Entity
+@Audited
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
-public abstract class SpecimenOrObservationBase extends IdentifyableMediaEntity{
+@Table(appliesTo="SpecimenOrObservationBase", indexes = { @Index(name = "specimenOrObservationBaseTitleCacheIndex", columnNames = { "titleCache" }) })
+public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableMediaEntity<S> {
+
private static final Logger logger = Logger.getLogger(SpecimenOrObservationBase.class);
+ @XmlElementWrapper(name = "Descriptions")
+ @XmlElement(name = "Description")
+ @ManyToMany(fetch = FetchType.LAZY,mappedBy="describedSpecimenOrObservations",targetEntity=DescriptionBase.class)
+ @Cascade(CascadeType.SAVE_UPDATE)
+ @NotNull
private Set<DescriptionBase> descriptions = new HashSet<DescriptionBase>();
+
+ @XmlElementWrapper(name = "Determinations")
+ @XmlElement(name = "Determination")
+ @OneToMany(mappedBy="identifiedUnit")
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
+ @IndexedEmbedded(depth = 2)
+ @NotNull
private Set<DeterminationEvent> determinations = new HashSet<DeterminationEvent>();
+
+ @XmlElement(name = "Sex")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToOne(fetch = FetchType.LAZY)
private Sex sex;
+
+ @XmlElement(name = "LifeStage")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToOne(fetch = FetchType.LAZY)
private Stage lifeStage;
+
+ @XmlElement(name = "IndividualCount")
+ @Field(index=org.hibernate.search.annotations.Index.UN_TOKENIZED)
+ @Min(0)
private Integer individualCount;
+
// the verbatim description of this occurrence. Free text usable when no atomised data is available.
// in conjunction with titleCache which serves as the "citation" string for this object
- private MultilanguageSet description;
+ @XmlElement(name = "Description")
+ @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
+ @IndexedEmbedded
+ @NotNull
+ protected Map<Language,LanguageString> description = new HashMap<Language,LanguageString>();
+
// events that created derivedUnits from this unit
- private Set<DerivationEvent> derivationEvents = new HashSet();
+ @XmlElementWrapper(name = "DerivationEvents")
+ @XmlElement(name = "DerivationEvent")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToMany(fetch=FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
+ @NotNull
+ protected Set<DerivationEvent> derivationEvents = new HashSet<DerivationEvent>();
/**
* Constructor
super();
}
- @ManyToMany
- @Cascade( { CascadeType.SAVE_UPDATE })
+ /**
+ * The descriptions this specimen or observation is part of.<BR>
+ * A specimen can not only have it's own {@link SpecimenDescription specimen description }
+ * but can also be part of a {@link TaxonDescription taxon description} or a
+ * {@link TaxonNameDescription taxon name description}.<BR>
+ * @see #getSpecimenDescriptions()
+ * @return
+ */
public Set<DescriptionBase> getDescriptions() {
+ if(descriptions == null) {
+ this.descriptions = new HashSet<DescriptionBase>();
+ }
return this.descriptions;
}
- protected void setDescriptions(Set<DescriptionBase> descriptions) {
- this.descriptions = descriptions;
+
+ /**
+ * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
+ * @see #getDescriptions()
+ * @return
+ */
+ @Transient
+ public Set<SpecimenDescription> getSpecimenDescriptions() {
+ return getSpecimenDescriptions(true);
+ }
+
+ /**
+ * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
+ * @see #getDescriptions()
+ * @return
+ */
+ @Transient
+ public Set<SpecimenDescription> getSpecimenDescriptions(boolean includeImageGallery) {
+ Set<SpecimenDescription> specimenDescriptions = new HashSet<SpecimenDescription>();
+ for (DescriptionBase descriptionBase : getDescriptions()){
+ if (descriptionBase.isInstanceOf(SpecimenDescription.class)){
+ if (includeImageGallery || descriptionBase.isImageGallery() == false){
+ specimenDescriptions.add(descriptionBase.deproxy(descriptionBase, SpecimenDescription.class));
+ }
+
+ }
+ }
+ return specimenDescriptions;
+ }
+ /**
+ * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
+ * @see #getDescriptions()
+ * @return
+ */
+ @Transient
+ public Set<SpecimenDescription> getSpecimenDescriptionImageGallery() {
+ Set<SpecimenDescription> specimenDescriptions = new HashSet<SpecimenDescription>();
+ for (DescriptionBase descriptionBase : getDescriptions()){
+ if (descriptionBase.isInstanceOf(SpecimenDescription.class)){
+ if (descriptionBase.isImageGallery() == true){
+ specimenDescriptions.add(descriptionBase.deproxy(descriptionBase, SpecimenDescription.class));
+ }
+ }
+ }
+ return specimenDescriptions;
}
+
+ /**
+ * Adds a new description to this specimen or observation
+ * @param description
+ */
public void addDescription(DescriptionBase description) {
this.descriptions.add(description);
+ if (! description.getDescribedSpecimenOrObservations().contains(this)){
+ description.addDescribedSpecimenOrObservation(this);
+ }
+// Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "addDescribedSpecimenOrObservation", new Class[] {SpecimenOrObservationBase.class});
+// ReflectionUtils.makeAccessible(method);
+// ReflectionUtils.invokeMethod(method, description, new Object[] {this});
}
+
+ /**
+ * Removes a specimen from a description (removes a description from this specimen)
+ * @param description
+ */
public void removeDescription(DescriptionBase description) {
this.descriptions.remove(description);
+ if (description.getDescribedSpecimenOrObservations().contains(this)){
+ description.removeDescribedSpecimenOrObservation(this);
+ }
+// Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "removeDescribedSpecimenOrObservations", new Class[] {SpecimenOrObservationBase.class});
+// ReflectionUtils.makeAccessible(method);
+// ReflectionUtils.invokeMethod(method, description, new Object[] {this});
}
- @ManyToMany
- @Cascade( { CascadeType.SAVE_UPDATE })
public Set<DerivationEvent> getDerivationEvents() {
+ if(derivationEvents == null) {
+ this.derivationEvents = new HashSet<DerivationEvent>();
+ }
return this.derivationEvents;
}
- protected void setDerivationEvents(Set<DerivationEvent> derivationEvents) {
- this.derivationEvents = derivationEvents;
- }
- public void addDerivationEvent(DerivationEvent event) {
- this.derivationEvents.add(event);
+
+ public void addDerivationEvent(DerivationEvent derivationEvent) {
+ if (! this.derivationEvents.contains(derivationEvent)){
+ this.derivationEvents.add(derivationEvent);
+ derivationEvent.addOriginal(this);
+ }
}
- public void removeDerivationEvent(DerivationEvent event) {
- this.derivationEvents.remove(event);
+
+ public void removeDerivationEvent(DerivationEvent derivationEvent) {
+ this.derivationEvents.remove(derivationEvent);
}
-
-
- @OneToMany(mappedBy="identifiedUnit")
- @Cascade({CascadeType.SAVE_UPDATE})
public Set<DeterminationEvent> getDeterminations() {
+ if(determinations == null) {
+ this.determinations = new HashSet<DeterminationEvent>();
+ }
return this.determinations;
}
- protected void setDeterminations(Set<DeterminationEvent> determinations) {
- this.determinations = determinations;
- }
+
public void addDetermination(DeterminationEvent determination) {
// FIXME bidirectional integrity. Use protected Determination setter
this.determinations.add(determination);
}
+
public void removeDetermination(DeterminationEvent determination) {
// FIXME bidirectional integrity. Use protected Determination setter
this.determinations.remove(determination);
}
-
- @ManyToOne
public Sex getSex() {
return sex;
}
this.sex = sex;
}
- @ManyToOne
public Stage getLifeStage() {
return lifeStage;
}
this.lifeStage = lifeStage;
}
-
+ @Override
public String generateTitle(){
- return "";
+ return getCacheStrategy().getTitleCache(this);
}
-
-
+
public Integer getIndividualCount() {
return individualCount;
}
this.individualCount = individualCount;
}
-
- public MultilanguageSet getDefinition(){
+ public Map<Language,LanguageString> getDefinition(){
return this.description;
}
- private void setDefinition(MultilanguageSet description){
- this.description = description;
- }
+
public void addDefinition(LanguageString description){
- this.description.put(description);
+ this.description.put(description.getLanguage(),description);
}
- public void addDefinition(String text, Language lang){
- this.description.put(text, lang);
+
+ public void addDefinition(String text, Language language){
+ this.description.put(language, LanguageString.NewInstance(text, language));
}
public void removeDefinition(Language lang){
this.description.remove(lang);
}
-
/**
* for derived units get the single next higher parental/original unit.
* If multiple original units exist throw error
*/
@Transient
public SpecimenOrObservationBase getOriginalUnit(){
+ logger.warn("GetOriginalUnit not yet implemented");
return null;
}
- @Transient
- public abstract GatheringEvent getGatheringEvent();
+//******************** CLONE **********************************************/
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
+ * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()
+ * @see java.lang.Object#clone()
+ */
+ @Override
+ public Object clone() throws CloneNotSupportedException {
+ SpecimenOrObservationBase result = null;
+ result = (SpecimenOrObservationBase)super.clone();
+
+ //defininion (description, languageString)
+ result.description = new HashMap<Language,LanguageString>();
+ for(LanguageString languageString : this.description.values()) {
+ LanguageString newLanguageString = (LanguageString)languageString.clone();
+ result.addDefinition(newLanguageString);
+ }
+
+ //sex
+ result.setSex(this.sex);
+ //life stage
+ result.setLifeStage(this.lifeStage);
+
+ //Descriptions
+ for(DescriptionBase description : this.descriptions) {
+ result.addDescription((SpecimenDescription)description);
+ }
+
+ //DeterminationEvent FIXME should clone() the determination
+ // as the relationship is OneToMany
+ for(DeterminationEvent determination : this.determinations) {
+ result.addDetermination(determination);
+ }
+
+ //DerivationEvent
+ for(DerivationEvent derivationEvent : this.derivationEvents) {
+ result.addDerivationEvent(derivationEvent);
+ }
+
+ //no changes to: individualCount
+ return result;
+ }
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff