/**
* 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.occurrence;
-import java.lang.reflect.Method;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import javax.persistence.Column;
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.MapKeyJoinColumn;
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.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlIDREF;
import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.Index;
import org.hibernate.annotations.Table;
+import org.hibernate.annotations.Type;
import org.hibernate.envers.Audited;
+import org.hibernate.search.annotations.Analyze;
+import org.hibernate.search.annotations.ContainedIn;
import org.hibernate.search.annotations.Field;
import org.hibernate.search.annotations.IndexedEmbedded;
-import org.springframework.util.ReflectionUtils;
+import org.hibernate.search.annotations.NumericField;
import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
+import eu.etaxonomy.cdm.model.common.DefinedTerm;
+import eu.etaxonomy.cdm.model.common.IMultiLanguageTextHolder;
+import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.LanguageString;
+import eu.etaxonomy.cdm.model.common.MultilanguageText;
+import eu.etaxonomy.cdm.model.common.TermType;
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 eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
/**
* type figures are observations with at least a figure object in media
* @author m.doering
- * @version 1.0
* @created 08-Nov-2007 13:06:41
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "SpecimenOrObservationBase", propOrder = {
+ "recordBasis",
+ "publish",
"sex",
- "individualCount",
- "lifeStage",
- "description",
+ "lifeStage",
+ "kindOfUnit",
+ "individualCount",
+ "definition",
"descriptions",
"determinations",
"derivationEvents"
@Audited
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
@Table(appliesTo="SpecimenOrObservationBase", indexes = { @Index(name = "specimenOrObservationBaseTitleCacheIndex", columnNames = { "titleCache" }) })
-public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableMediaEntity<S> {
-
+public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> implements IMultiLanguageTextHolder{
+ private static final long serialVersionUID = 6932680139334408031L;
private static final Logger logger = Logger.getLogger(SpecimenOrObservationBase.class);
+
+ /**
+ * An indication of what the unit record describes.
+ *
+ * NOTE: The name of the attribute was chosen against the common naming conventions of the CDM
+ * as it is well known in common standards like ABCD and DarwinCore. According to CDM naming
+ * conventions it would specimenOrObservationType.
+ *
+ * @see ABCD: DataSets/DataSet/Units/Unit/RecordBasis
+ * @see Darwin Core: http://wiki.tdwg.org/twiki/bin/view/DarwinCore/BasisOfRecord
+ */
+ @XmlAttribute(name ="RecordBasis")
+ @Column(name="recordBasis")
+ @NotNull
+ @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
+ parameters = {@org.hibernate.annotations.Parameter(name = "enumClass", value = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType")}
+ )
+ private SpecimenOrObservationType recordBasis;
+
@XmlElementWrapper(name = "Descriptions")
@XmlElement(name = "Description")
- @ManyToMany(fetch = FetchType.LAZY,mappedBy="describedSpecimenOrObservations",targetEntity=DescriptionBase.class)
+ @OneToMany(mappedBy="describedSpecimenOrObservation", fetch = FetchType.LAZY)
@Cascade(CascadeType.SAVE_UPDATE)
- @NotNull
+ @ContainedIn
+ @NotNull
private Set<DescriptionBase> descriptions = new HashSet<DescriptionBase>();
+
@XmlElementWrapper(name = "Determinations")
@XmlElement(name = "Determination")
- @OneToMany(mappedBy="identifiedUnit")
- @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ @OneToMany(mappedBy="identifiedUnit", orphanRemoval=true)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
@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;
-
+ private DefinedTerm sex;
+
@XmlElement(name = "LifeStage")
@XmlIDREF
@XmlSchemaType(name = "IDREF")
@ManyToOne(fetch = FetchType.LAZY)
- private Stage lifeStage;
+ private DefinedTerm lifeStage;
+ /**
+ * Part(s) of organism or class of materials represented by this unit.
+ * Example: fruits, seeds, tissue, gDNA, leaves
+ *
+ * @see ABCD: DataSets/DataSet/Units/Unit/KindOfUnit
+ * @see TermType#KindOfUnit
+ */
+ @XmlElement(name = "KindOfUnit")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToOne(fetch = FetchType.LAZY)
+// @IndexedEmbedded(depth=1)
+ private DefinedTerm kindOfUnit;
+
@XmlElement(name = "IndividualCount")
- @Field(index=org.hibernate.search.annotations.Index.UN_TOKENIZED)
+ @Field(analyze = Analyze.NO)
+ @NumericField
@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
@XmlElement(name = "Description")
@XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
- @OneToMany(fetch = FetchType.LAZY)
- @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
+ @OneToMany(fetch = FetchType.LAZY, orphanRemoval=true)
+ @MapKeyJoinColumn(name="definition_mapkey_id")
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE})
@IndexedEmbedded
@NotNull
- protected Map<Language,LanguageString> description = new HashMap<Language,LanguageString>();
-
+ protected Map<Language,LanguageString> definition = new HashMap<Language,LanguageString>();
+
// events that created derivedUnits from this unit
@XmlElementWrapper(name = "DerivationEvents")
@XmlElement(name = "DerivationEvent")
@XmlIDREF
@XmlSchemaType(name = "IDREF")
@ManyToMany(fetch=FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE})
@NotNull
protected Set<DerivationEvent> derivationEvents = new HashSet<DerivationEvent>();
+
+ @XmlAttribute(name = "publish")
+ private boolean publish = true;
+
+
+//********************************** CONSTRUCTOR *********************************/
+
+ //for hibernate use only
+ @Deprecated
+ protected SpecimenOrObservationBase(){super();}
+
+ protected SpecimenOrObservationBase(SpecimenOrObservationType recordBasis) {
+ super();
+ if (recordBasis == null){ throw new IllegalArgumentException("RecordBasis must not be null");}
+ this.recordBasis = recordBasis;
+ }
+
+//************************* GETTER / SETTER ***********************/
/**
- * Constructor
+ * @see #recordBasis
+ * @return
*/
- protected SpecimenOrObservationBase(){
- super();
+ public SpecimenOrObservationType getRecordBasis() {
+ return recordBasis;
+ }
+
+ /**
+ * @see #recordBasis
+ * @param recordBasis
+ */
+ public void setRecordBasis(SpecimenOrObservationType recordBasis) {
+ this.recordBasis = recordBasis;
}
+
+ /**
+ * Returns the boolean value indicating if this specimen or observation should be withheld
+ * (<code>publish=false</code>) or not (<code>publish=true</code>) during any publication
+ * process to the general public.
+ * This publish flag implementation is preliminary and may be replaced by a more general
+ * implementation of READ rights in future.<BR>
+ * The default value is <code>true</code>.
+ */
+ public boolean isPublish() {
+ return publish;
+ }
+
+ /**
+ * @see #isPublish()
+ * @param publish
+ */
+ public void setPublish(boolean publish) {
+ this.publish = publish;
+ }
+
+ /**
+ * 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;
}
+ /**
+ * 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} which act as an image gallery
+ * and which 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);
+ if (description.getDescribedSpecimenOrObservation() != null){
+ description.getDescribedSpecimenOrObservation().removeDescription(description);
}
-// Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "addDescribedSpecimenOrObservation", new Class[] {SpecimenOrObservationBase.class});
-// ReflectionUtils.makeAccessible(method);
-// ReflectionUtils.invokeMethod(method, description, new Object[] {this});
+ descriptions.add(description);
+ description.setDescribedSpecimenOrObservation(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});
+ boolean existed = descriptions.remove(description);
+ if (existed){
+ description.setDescribedSpecimenOrObservation(null);
+ }
}
-
+
public Set<DerivationEvent> getDerivationEvents() {
if(derivationEvents == null) {
this.derivationEvents = new HashSet<DerivationEvent>();
}
return this.derivationEvents;
}
-
+
public void addDerivationEvent(DerivationEvent derivationEvent) {
if (! this.derivationEvents.contains(derivationEvent)){
this.derivationEvents.add(derivationEvent);
derivationEvent.addOriginal(this);
}
}
-
+
public void removeDerivationEvent(DerivationEvent derivationEvent) {
this.derivationEvents.remove(derivationEvent);
}
-
+
public Set<DeterminationEvent> getDeterminations() {
if(determinations == null) {
this.determinations = new HashSet<DeterminationEvent>();
// 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);
}
-
- public Sex getSex() {
+
+ public DefinedTerm getSex() {
return sex;
}
- public void setSex(Sex sex) {
+ public void setSex(DefinedTerm sex) {
this.sex = sex;
}
- public Stage getLifeStage() {
+ public DefinedTerm getLifeStage() {
return lifeStage;
}
- public void setLifeStage(Stage lifeStage) {
+ public void setLifeStage(DefinedTerm lifeStage) {
this.lifeStage = lifeStage;
}
+
+ /**
+ * @see #kindOfUnit
+ * @return
+ */
+ public DefinedTerm getKindOfUnit() {
+ return kindOfUnit;
+ }
+
+ /**
+ * @see #kindOfUnit
+ * @param kindOfUnit
+ */
+ public void setKindOfUnit(DefinedTerm kindOfUnit) {
+ this.kindOfUnit = kindOfUnit;
+ }
+
@Override
public String generateTitle(){
- logger.warn("Generate title for specimen not yet implemented");
- return "";
+ return getCacheStrategy().getTitleCache(this);
}
-
+
public Integer getIndividualCount() {
return individualCount;
}
}
public Map<Language,LanguageString> getDefinition(){
- return this.description;
+ return this.definition;
}
-
- public void addDefinition(LanguageString description){
- this.description.put(description.getLanguage(),description);
+
+ /**
+ * adds the {@link LanguageString description} to the {@link MultilanguageText multilanguage text}
+ * used to define <i>this</i> specimen or observation.
+ *
+ * @param description the languageString in with the title string and the given language
+ *
+ * @see #getDefinition()
+ * @see #putDefinition(Language, String)
+ */
+ public void putDefinition(LanguageString description){
+ this.definition.put(description.getLanguage(),description);
}
-
- public void addDefinition(String text, Language language){
- this.description.put(language, LanguageString.NewInstance(text, language));
+
+ /**
+ * Creates a {@link LanguageString language string} based on the given text string
+ * and the given {@link Language language} and adds it to the {@link MultilanguageText multilanguage text}
+ * used to define <i>this</i> specimen or observation.
+ *
+ * @param language the language in which the title string is formulated
+ * @param text the definition in a particular language
+ *
+ * @see #getDefinition()
+ * @see #putDefinition(LanguageString)
+ */
+ public void putDefinition(Language language, String text){
+ this.definition.put(language, LanguageString.NewInstance(text, language));
}
+
+
public void removeDefinition(Language lang){
- this.description.remove(lang);
+ this.definition.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()
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()) {
+ result.definition = new HashMap<Language,LanguageString>();
+ for(LanguageString languageString : this.definition.values()) {
LanguageString newLanguageString = (LanguageString)languageString.clone();
- result.addDefinition(newLanguageString);
- }
+ result.putDefinition(newLanguageString);
+ }
//sex
result.setSex(this.sex);
//life stage
result.setLifeStage(this.lifeStage);
-
+
//Descriptions
for(DescriptionBase description : this.descriptions) {
- result.addDescription((SpecimenDescription)description);
+ result.addDescription(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