package eu.etaxonomy.cdm.jaxb;\r
\r
import java.io.File;\r
-import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.io.Writer;\r
\r
-import javax.xml.XMLConstants;\r
import javax.xml.bind.JAXBContext;\r
import javax.xml.bind.JAXBException;\r
import javax.xml.bind.Marshaller;\r
import javax.xml.bind.Unmarshaller;\r
-import javax.xml.transform.Source;\r
-import javax.xml.transform.stream.StreamSource;\r
-import javax.xml.validation.Schema;\r
-import javax.xml.validation.SchemaFactory;\r
-\r
import org.apache.commons.logging.Log;\r
import org.apache.commons.logging.LogFactory;\r
import org.xml.sax.SAXException;\r
\r
import eu.etaxonomy.cdm.model.DataSet;\r
-import eu.etaxonomy.cdm.strategy.cache.reference.BookDefaultCacheStrategy;\r
\r
/*\r
Initializes a JaxbContext with one class (eu.etaxonomy.cdm.model.DataSet) \r
\r
import org.apache.commons.logging.Log;\r
import org.apache.commons.logging.LogFactory;\r
-import org.apache.log4j.Logger;\r
import org.apache.xml.resolver.CatalogManager;\r
import org.apache.xml.resolver.tools.CatalogResolver;\r
import org.w3c.dom.ls.LSInput;\r
import java.io.IOException;\r
import java.io.StringReader;\r
import java.io.StringWriter;\r
-import java.io.Writer;\r
-\r
import javax.xml.bind.JAXBContext;\r
import javax.xml.bind.JAXBException;\r
import javax.xml.bind.SchemaOutputResolver;\r
\r
package eu.etaxonomy.cdm.jaxb;\r
\r
-import java.util.UUID;\r
-\r
import javax.xml.bind.annotation.adapters.XmlAdapter;\r
\r
import org.apache.log4j.Logger;\r
package eu.etaxonomy.cdm.model;\r
\r
-import java.util.ArrayList;\r
import java.util.Collection;\r
import java.util.HashSet;\r
import java.util.List;\r
import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;\r
import eu.etaxonomy.cdm.model.agent.Person;\r
import eu.etaxonomy.cdm.model.agent.Team;\r
-import eu.etaxonomy.cdm.model.common.IRelated;\r
import eu.etaxonomy.cdm.model.common.Keyword;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
import eu.etaxonomy.cdm.model.common.TermBase;\r
public Collection<TaxonBase> getTaxonBases() {\r
\r
// FIXME: This is a dirty trick.\r
- Object obj = (Object)taxa;\r
+ Object obj = taxa;\r
Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;\r
return taxonBases;\r
}\r
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.XmlRootElement;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
/**
* Allows to hold one {@link Institution institution} to which a {@link Person person} is affiliated.
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.XmlType;
/**
\r
import org.apache.log4j.Logger;\r
\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
import eu.etaxonomy.cdm.strategy.cache.agent.INomenclaturalAuthorCacheStrategy;\r
\r
\r
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import eu.etaxonomy.cdm.model.media.Rights;
-
import java.util.*;
import javax.persistence.*;
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.common.VersionableEntity#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
AnnotatableEntity result = (AnnotatableEntity)super.clone();
//Annotations
Set<Annotation> newAnnotations = getNewAnnotationSet();
for (Annotation annotation : this.annotations ){
- Annotation newExtension = (Annotation)annotation.clone(this);
+ Annotation newExtension = annotation.clone(this);
newAnnotations.add(newExtension);
}
result.setAnnotations(newAnnotations);
//Markers
Set<Marker> newMarkers = getNewMarkerSet();
for (Marker marker : this.markers ){
- Marker newMarker = (Marker)marker.clone(this);
+ Marker newMarker = marker.clone(this);
newMarkers.add(newMarker);
}
result.setMarkers(newMarkers);
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
Annotation result = (Annotation)super.clone();
//no changes to: type, flag
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
CdmBase result = (CdmBase)super.clone();
import eu.etaxonomy.cdm.model.common.init.DefaultVocabularyStore;
import eu.etaxonomy.cdm.model.common.init.IVocabularyStore;
import eu.etaxonomy.cdm.model.media.Media;
-import eu.etaxonomy.cdm.model.name.Rank;
-
import java.lang.reflect.Field;
import java.util.*;
package eu.etaxonomy.cdm.model.common;
-import javax.persistence.Entity;
import javax.persistence.ManyToOne;
import javax.persistence.MappedSuperclass;
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
Extension result = (Extension)super.clone();
//no changes to: type, value
import org.apache.log4j.Logger;
-import java.util.*;
import javax.persistence.*;
/**
import javax.persistence.ManyToOne;\r
import javax.persistence.Temporal;\r
import javax.persistence.TemporalType;\r
-import javax.persistence.Transient;\r
-\r
import org.hibernate.annotations.Cascade;\r
import org.hibernate.annotations.CascadeType;\r
import org.joda.time.DateTime;\r
\r
import eu.etaxonomy.cdm.model.media.Rights;\r
\r
-import org.apache.log4j.Logger;\r
-\r
public interface IIdentifiableEntitiy<T extends IdentifiableEntity> {\r
\r
public abstract String getLsid();\r
\r
package eu.etaxonomy.cdm.model.common;\r
\r
-import org.apache.log4j.Logger;\r
-\r
/**\r
* @author a.mueller\r
* @created 21.05.2008\r
/* (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();
for (Extension extension : this.extensions ){
- Extension newExtension = (Extension)extension.clone(this);
+ Extension newExtension = extension.clone(this);
newExtensions.add(newExtension);
}
result.setExtensions(newExtensions);
//OriginalSources
Set<OriginalSource> newOriginalSources = getNewOriginalSourcesSet();
for (OriginalSource originalSource : this.sources){
- OriginalSource newSource = (OriginalSource)originalSource.clone(this);
+ OriginalSource newSource = originalSource.clone(this);
newOriginalSources.add(newSource);
}
result.setSources(newOriginalSources);
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.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
/**
return result;
}
+ @Override
public void writeCsvLine(CSVWriter writer) {
String [] line = new String[6];
line[0] = getUuid().toString();
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
Marker result = (Marker)super.clone();
//no changes to: type, flag
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
-
import java.util.*;
import javax.persistence.*;
package eu.etaxonomy.cdm.model.common;
-import java.util.Enumeration;
import java.util.HashMap;
import java.util.List;
-import java.util.Locale;
-
import org.apache.log4j.Logger;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.XmlType;
import javax.persistence.*;
}
}
+ @Override
public boolean equals(Object o){
if (! OrderedTermBase.class.isAssignableFrom(o.getClass())){
return false;
if (sortedTerms.size() == 0){\r
lowestOrderIndex = 0;\r
}else{\r
- Object first = (T)sortedTerms.first();\r
+ Object first = sortedTerms.first();\r
lowestOrderIndex = ((T)first).orderIndex;\r
}\r
term.orderIndex = lowestOrderIndex + 1;\r
package eu.etaxonomy.cdm.model.common;
-import org.hibernate.annotations.CascadeType;
import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
import javax.persistence.Transient;
import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
/**
* Other names/labels/titles (abreviated or not) for the same object (person,
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
OriginalSource result = (OriginalSource)super.clone();
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import java.util.*;
import javax.persistence.*;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
ReferencedEntityBase result = (ReferencedEntityBase)super.clone();
package eu.etaxonomy.cdm.model.common;
-import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
import eu.etaxonomy.cdm.model.taxon.Taxon;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
-
import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import javax.persistence.*;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAnyElement;
import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlElementRef;
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;
/**
return this.getInverseRepresentation(lang).getDescription();
}
+ @Override
public ILoadableTerm readCsvLine(List csvLine) {
RelationshipTermBase result;
// read UUID, URI, english label+description
- List<String> csvLineString = (List<String>)csvLine;
+ List<String> csvLineString = csvLine;
result = (RelationshipTermBase)super.readCsvLine(csvLineString);
// inverse label + 2 booleans
String inverseText = csvLineString.get(5).trim();
return result;
}
+ @Override
public void writeCsvLine(CSVWriter writer) {
String [] line = new String[8];
line[0] = getUuid().toString();
}
+ @Override
public String toString(){
// we dont need the language returned too, do we?
return getLabel();
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.XmlType;
import org.apache.log4j.Logger;
return null;
}
public static final TermVocabulary getUUID(UUID uuid){
- return (TermVocabulary)findByUuid(uuid);
+ return findByUuid(uuid);
}
public static final TermVocabulary LANGUAGE(){
return getUUID(uuidLanguage);
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.model.reference.Generic;
-
/**
* @author m.doering
* @version 1.0
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
+ @Override
public TimePeriod clone() {
try {
TimePeriod result = (TimePeriod)super.clone();
* The createdWhen is set to the current date.
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
VersionableEntity result = (VersionableEntity)super.clone();
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
import eu.etaxonomy.cdm.model.location.NamedAreaType;
-import eu.etaxonomy.cdm.model.location.TdwgArea;
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
import eu.etaxonomy.cdm.model.common.OrderedTermBase;
-import eu.etaxonomy.cdm.model.common.TermVocabulary;
-
import org.apache.log4j.Logger;
-import java.util.*;
import javax.persistence.*;
/**
package eu.etaxonomy.cdm.model.description;
-import java.util.HashMap;
import java.util.Map;
import eu.etaxonomy.cdm.model.common.Language;
import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.CollectionOfElements;
-
import javax.persistence.*;
/**
import org.apache.log4j.Logger;\r
import org.jdom.Element;\r
import org.jdom.Namespace;\r
-import org.jdom.filter.Filter;\r
-\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
import eu.etaxonomy.cdm.common.XmlHelp;\r
import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
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.XmlSchemaType;
/**
* +/- current ISO codes. year given with each entry
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import eu.etaxonomy.cdm.model.common.Extension;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;
@MappedSuperclass
public abstract class IdentifyableMediaEntity extends IdentifiableEntity implements IMediaDocumented, IMediaEntity{
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
IdentifyableMediaEntity result = (IdentifyableMediaEntity)super.clone();
//Media
import java.util.ArrayList;
import java.util.List;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import eu.etaxonomy.cdm.model.occurrence.Collection;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import org.apache.log4j.Logger;
import java.util.*;
import eu.etaxonomy.cdm.model.common.VersionableEntity;
import org.apache.log4j.Logger;
-import java.util.*;
import javax.persistence.*;
/**
import eu.etaxonomy.cdm.model.common.VersionableEntity;
import org.apache.log4j.Logger;
-import java.util.*;
import javax.persistence.*;
/**
this.citationMicroReference = citationMicroReference;
}
+ @Override
public String generateTitle(){
return "";
}
* @see TaxonNameBase#addRelationship(RelationshipBase)
* @see TaxonNameBase#addNameRelationship(NameRelationship)
*/
+ @Override
@Deprecated //To be used by RelationshipBase only
public void addRelationship(RelationshipBase relation) {
if (relation instanceof HybridRelationship){
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
-
import javax.persistence.*;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
package eu.etaxonomy.cdm.model.name;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import org.hibernate.annotations.CascadeType;
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
-import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
import eu.etaxonomy.cdm.model.taxon.Synonym;
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonComparator;
import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
/**
*/
@Override
public ILoadableTerm readCsvLine(List csvLine_, Language lang) {
- List<String> csvLine = (List<String>) csvLine_;
+ List<String> csvLine = csvLine_;
this.setUuid(UUID.fromString(csvLine.get(0)));
this.setUri(csvLine.get(1));
String label = csvLine.get(2).trim();
import eu.etaxonomy.cdm.model.common.IRelated;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.common.RelationshipBase;
-import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
@Cascade({CascadeType.SAVE_UPDATE})
@Target(ReferenceBase.class)
public INomenclaturalReference getNomenclaturalReference(){
- return (INomenclaturalReference) this.nomenclaturalReference;
+ return this.nomenclaturalReference;
}
/**
* Assigns a nomenclatural {@link reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
import eu.etaxonomy.cdm.model.common.OrderedTermBase;
-import eu.etaxonomy.cdm.model.common.TermVocabulary;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
-
import org.apache.log4j.Logger;
import java.util.*;
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
-import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;
-
import javax.persistence.*;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import eu.etaxonomy.cdm.model.agent.Institution;
-import eu.etaxonomy.cdm.model.description.Scope;
import eu.etaxonomy.cdm.model.media.IdentifyableMediaEntity;
import org.apache.log4j.Logger;
this.townOrLocation = townOrLocation;
}
+ @Override
public String generateTitle(){
return "";
}
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 eu.etaxonomy.cdm.model.media.IdentifyableMediaEntity;
}
+ @Override
public String generateTitle(){
return "";
}
* @see NomenclaturalReferenceHelper#getCitation()
* @see StrictReferenceBase#getCitation()
*/
+ @Override
@Transient
public String getCitation(){
return nomRefBase.getCitation();
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Article clone(){
Article result = (Article)super.clone();
//no changes to: inJournal, pages, series, volume
import org.apache.log4j.Logger;
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
/**
* The class representing types (categories) of {@link BibtexReference BibTeX references}
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.strategy.cache.reference.BibtexDefaultCacheStrategy;
/**
*
* @return the string with the year of publication
*/
+ @Override
public String getYear(){
return this.year;
}
*
* @see NomenclaturalReferenceHelper#getCitation()
*/
+ @Override
@Transient
public String getCitation(){
return nomRefBase.getCitation();
* @see common.IdentifiableEntity#getTitleCache()
* @see common.IdentifiableEntity#generateTitle()
*/
+ @Override
public String generateTitle(){
return nomRefBase.generateTitle();
}
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.strategy.cache.reference.BookDefaultCacheStrategy;
/**
* @see NomenclaturalReferenceHelper#getCitation()
* @see StrictReferenceBase#getCitation()
*/
+ @Override
@Transient
public String getCitation(){
return nomRefBase.getCitation();
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Book clone(){
Book result = (Book)super.clone();
//no changes to: edition, isbn
* @see NomenclaturalReferenceHelper#getCitation()
* @see StrictReferenceBase#getCitation()
*/
+ @Override
@Transient
public String getCitation(){
return nomRefBase.getCitation();
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public BookSection clone(){
BookSection result = (BookSection)super.clone();
//no changes to: inBook
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public CdDvd clone(){
CdDvd result = (CdDvd)super.clone();
//no changes to: -
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Database clone(){
Database result = (Database)super.clone();
//no changes to: -
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
-import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.strategy.cache.reference.GenericDefaultCacheStrategy;
/**
* @see NomenclaturalReferenceHelper#getCitation()
* @see StrictReferenceBase#getCitation()
*/
+ @Override
@Transient
public String getCitation(){
return nomRefBase.getCitation();
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Generic clone(){
Generic result = (Generic)super.clone();
//no changes to: editor, pages, placePublished,publisher, series, volume
import javax.persistence.Transient;
import eu.etaxonomy.cdm.model.common.IIdentifiableEntitiy;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
/**
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-
/**
* This class represents isolated parts (usually papers or abstracts) within
* {@link Proceedings conference proceedings}.
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Journal clone(){
return (Journal)super.clone();
}
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.reference.PublicationBase#clone()
*/
+ @Override
public Map clone(){
Map result = (Map)super.clone();
//no changes to: -
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.strategy.cache.reference.INomenclaturalReferenceCacheStrategy;\r
\r
/**\r
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.reference.PublicationBase#clone()
*/
+ @Override
public Patent clone(){
Patent result = (Patent)super.clone();
//no changes to: -
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.reference.PublicationBase#clone()
*/
+ @Override
public PersonalCommunication clone(){
PersonalCommunication result = (PersonalCommunication)super.clone();
//no changes to: -
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.reference.PublicationBase#clone()
*/
+ @Override
public PrintSeries clone(){
PrintSeries result = (PrintSeries)super.clone();
//no changes to: series
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone(){
PrintedUnitBase result = (PrintedUnitBase)super.clone();
//no changes to: editor, inSeries, pages, volume, seriesPart
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Proceedings clone(){
Proceedings result = (Proceedings)super.clone();
//no changes to: organization
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone(){
PublicationBase result = (PublicationBase)super.clone();
//no changes to: placePublished, publisher
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.model.common.IParsable;
import eu.etaxonomy.cdm.model.media.IdentifyableMediaEntity;
-import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.strategy.cache.reference.IReferenceBaseCacheStrategy;
/**
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() throws CloneNotSupportedException{
ReferenceBase result = (ReferenceBase)super.clone();
//no changes to: authorTeam, hasProblem, nomenclaturallyRelevant, uri
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.reference.PublicationBase#clone()
*/
+ @Override
public Report clone(){
Report result = (Report)super.clone();
//no changes to: institution
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone(){
SectionBase result = (SectionBase)super.clone();
//no changes to: pages
*
* @see #getTitle()
*/
+ @Override
@Transient
// TODO implement
public String getCitation(){
* of <i>this</i> reference. The string is obtained by transformation of
* the {@link #getDatePublished() datePublished} attribute.
*/
+ @Override
@Transient
public String getYear(){
if (this.getDatePublished() == null){
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public Object clone() {
try {
StrictReferenceBase result = (StrictReferenceBase)super.clone();
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.reference.PublicationBase#clone()
*/
+ @Override
public Thesis clone(){
Thesis result = (Thesis)super.clone();
//no changes to: institution
* @see media.IdentifyableMediaEntity#clone()
* @see java.lang.Object#clone()
*/
+ @Override
public WebPage clone(){
WebPage result = (WebPage)super.clone();
//no changes to: -
import eu.etaxonomy.cdm.model.common.IRelated;
import eu.etaxonomy.cdm.model.common.RelationshipBase;
import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
-import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
import org.apache.log4j.Logger;
import org.apache.log4j.Logger;
import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
-import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
/**
* The class representing categories of {@link SynonymRelationship synonym relationships}
import eu.etaxonomy.cdm.model.common.RelationshipBase;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
-import eu.etaxonomy.cdm.model.name.NameRelationship;
-import eu.etaxonomy.cdm.model.name.NameRelationshipType;
-import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
-import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;
-import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
import org.apache.log4j.Logger;
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;
/**
package eu.etaxonomy.cdm.model.taxon;
import java.lang.reflect.Method;
-import java.util.List;
-
import javax.persistence.Entity;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import org.hibernate.annotations.Table;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
-import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
-import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
\r
import org.apache.log4j.Logger;\r
\r
-import eu.etaxonomy.cdm.model.common.TimePeriod;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
package eu.etaxonomy.cdm.model.taxon;
import eu.etaxonomy.cdm.model.common.RelationshipBase;
-import eu.etaxonomy.cdm.model.name.NameRelationshipType;
-import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
import org.apache.log4j.Logger;
package eu.etaxonomy.cdm.strategy.cache.agent;\r
\r
\r
-import eu.etaxonomy.cdm.model.agent.Team;\r
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;\r
\r
\r
import org.apache.log4j.Logger;\r
\r
-import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;\r
import eu.etaxonomy.cdm.model.agent.Person;\r
import eu.etaxonomy.cdm.model.agent.Team;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.strategy.StrategyBase;\r
\r
/**\r
\r
final static UUID uuid = UUID.fromString("1cdda0d1-d5bc-480f-bf08-40a510a2f223");\r
\r
+ @Override\r
public UUID getUuid(){\r
return uuid;\r
}\r
import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
\r
\r
/**\r
protected String ExAuthorSeperator = " ex ";\r
protected CharSequence BasionymAuthorCombinationAuthorSeperator = " ";\r
\r
+ @Override\r
public UUID getUuid(){\r
return uuid;\r
}\r
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.model.agent.Agent;\r
import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
\r
public class ZooNameDefaultCacheStrategy <T extends ZoologicalName> extends NonViralNameDefaultCacheStrategy<T> implements INonViralNameCacheStrategy<T> {\r
\r
protected String AuthorYearSeperator = ", ";\r
\r
+ @Override\r
public UUID getUuid(){\r
return uuid;\r
}\r
super();\r
}\r
\r
+ @Override\r
protected String getNomRefTitleWithoutYearAndAuthor(T article){\r
if (article == null){\r
return null;\r
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.model.reference.Article;\r
import eu.etaxonomy.cdm.model.reference.BibtexReference;\r
-import eu.etaxonomy.cdm.model.reference.Book;\r
-import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
-import eu.etaxonomy.cdm.strategy.StrategyBase;\r
\r
public class BibtexDefaultCacheStrategy <T extends BibtexReference> extends NomRefDefaultCacheStrategyBase<T> implements INomenclaturalReferenceCacheStrategy<T> {\r
private static final Logger logger = Logger.getLogger(BibtexDefaultCacheStrategy.class);\r
super();\r
}\r
\r
+ @Override\r
protected String getNomRefTitleWithoutYearAndAuthor(T article){\r
\r
if (true){\r
}\r
\r
\r
+ @Override\r
public String getNomRefTitleWithoutYearAndAuthor(T nomenclaturalReference){\r
if (nomenclaturalReference == null){\r
return null;\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.strategy.cache.reference.INomenclaturalReferenceCacheStrategy#getTokenizedNomenclaturalTitel(eu.etaxonomy.cdm.model.reference.INomenclaturalReference)\r
*/\r
+ @Override\r
public String getTokenizedNomenclaturalTitel(T bookSection) {\r
if (bookSection.getInBook() == null){\r
return null;\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.strategy.cache.reference.INomenclaturalReferenceCacheStrategy#getTitleCache(eu.etaxonomy.cdm.model.reference.INomenclaturalReference)\r
*/\r
+ @Override\r
public String getTitleCache(T bookSection) {\r
if (bookSection.getInBook() == null){\r
return null;\r
super();\r
}\r
\r
+ @Override\r
protected String getNomRefTitleWithoutYearAndAuthor(T genericReference){\r
if (genericReference == null){\r
return null;\r
\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
-import eu.etaxonomy.cdm.model.reference.Generic;\r
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
import eu.etaxonomy.cdm.strategy.StrategyBase;\r
import eu.etaxonomy.cdm.model.reference.Generic;\r
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
-import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;\r
import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;\r
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
\r
private Object lastPropValue;
public void propertyChange(PropertyChangeEvent e){
- logger.debug("Property [" + (String)e.getPropertyName()
+ logger.debug("Property [" + e.getPropertyName()
+ "] changed from " + e.getOldValue()
+ " to " + e.getNewValue());
lastPropValue = e.getNewValue() == null ? null : e.getNewValue();
package eu.etaxonomy.cdm.model;\r
\r
import java.util.ArrayList;\r
-import java.util.Collection;\r
import java.util.GregorianCalendar;\r
import java.util.HashSet;\r
-import java.util.Iterator;\r
import java.util.List;\r
import java.util.Set;\r
\r
import eu.etaxonomy.cdm.model.agent.Institution;\r
import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;\r
import eu.etaxonomy.cdm.model.agent.Person;\r
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;\r
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
import eu.etaxonomy.cdm.model.common.Keyword;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
import eu.etaxonomy.cdm.model.common.TermBase;\r
import eu.etaxonomy.cdm.model.common.TimePeriod;\r
import eu.etaxonomy.cdm.model.common.VersionableEntity;\r
import eu.etaxonomy.cdm.model.name.BotanicalName;\r
-import eu.etaxonomy.cdm.model.name.HomotypicalGroup;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
import eu.etaxonomy.cdm.model.reference.Book;\r
import eu.etaxonomy.cdm.model.reference.Database;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
import eu.etaxonomy.cdm.model.taxon.Synonym;\r
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
-import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
\r
public class DataSetTest {\r
\r
\r
// Set<TaxonRelationship> taxonRelationships;\r
taxonRelationships = rootT.getTaxonRelations();\r
- Object obj = (Object)taxonRelationships;\r
+ Object obj = taxonRelationships;\r
relationshipBases = (Set<RelationshipBase>)obj;\r
\r
}\r
public static void main(String[] args) {
DatabaseInitialiser dbInit = new DatabaseInitialiser();
- dbInit.insertTaxon("Abies alba");
- dbInit.insertTaxon("Polygala vulgaris");
+ DatabaseInitialiser.insertTaxon("Abies alba");
+ DatabaseInitialiser.insertTaxon("Polygala vulgaris");
}
}
import java.beans.PropertyChangeListener;\r
import java.beans.PropertyChangeSupport;\r
import java.lang.reflect.Field;\r
-import java.util.Calendar;\r
import java.util.UUID;\r
\r
import org.apache.log4j.Logger;\r
\r
static public class TestCdmBaseClass extends CdmBase{\r
public String testString = "testStringXsdfjlksj";\r
- public float testFloat = (float)1.43446E-5f;\r
+ public float testFloat = 1.43446E-5f;\r
public boolean testBoolean = false;\r
}\r
\r
\r
//Test\r
float oldValue = testCdm.testFloat;\r
- float newValue = (float)1.40239846E-4f;\r
+ float newValue = 1.40239846E-4f;\r
assertFalse(oldValue == newValue);\r
testCdm.firePropertyChange(prop, oldValue, newValue);\r
assertTrue(listener.isChanged());\r
@Test\r
public void testSetCreated() {\r
DateTime calendar = new DateTime();\r
- DateTime calendarTrue = (DateTime)calendar.withMillisOfSecond(23);\r
- DateTime calendarFalse = (DateTime)calendar.withMillisOfSecond(23);\r
+ DateTime calendarTrue = calendar.withMillisOfSecond(23);\r
+ DateTime calendarFalse = calendar.withMillisOfSecond(23);\r
calendarFalse = calendarFalse.plusMonths(5);\r
cdmBase.setCreated(calendar);\r
calendar = calendar.withMillisOfSecond(0);\r
\r
package eu.etaxonomy.cdm.model.common;\r
\r
-import static org.junit.Assert.*;\r
-\r
import org.apache.log4j.Logger;\r
import org.junit.After;\r
import org.junit.AfterClass;\r
import org.junit.BeforeClass;\r
import org.junit.Test;\r
\r
-import eu.etaxonomy.cdm.model.name.Rank;\r
-\r
/**\r
* @author a.mueller\r
* @created 23.04.2008\r
\r
import java.util.Iterator;\r
import java.util.Set;\r
-import java.util.SortedSet;\r
-\r
import org.apache.log4j.Logger;\r
import org.junit.After;\r
import org.junit.AfterClass;\r
import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
import eu.etaxonomy.cdm.model.common.WrongTermTypeException;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
-import eu.etaxonomy.cdm.test.suite.CdmTestSuite;\r
\r
/**\r
* @author AM\r
@Test\r
public void testDEFAULT_LANGUAGE() {\r
UUID uuidEnglish = UUID.fromString("e9f8cdb7-6819-44e8-95d3-e2d0690c3523");\r
- assertEquals(uuidEnglish, defaultVocabularyStore.DEFAULT_LANGUAGE().getUuid());\r
+ assertEquals(uuidEnglish, DefaultVocabularyStore.DEFAULT_LANGUAGE().getUuid());\r
}\r
\r
/**\r
import org.junit.AfterClass;\r
import org.junit.Before;\r
import org.junit.BeforeClass;\r
-import org.junit.Ignore;\r
import org.junit.Test;\r
\r
import eu.etaxonomy.cdm.model.agent.Team;\r
public TaxonNameBaseTestClass(Rank rank){super(rank);};\r
public TaxonNameBaseTestClass(HomotypicalGroup hg){super(hg);};\r
public TaxonNameBaseTestClass(Rank rank, HomotypicalGroup hg){super(rank, hg);};\r
+ @Override\r
public boolean isCodeCompliant(){return false;};\r
+ @Override\r
public void setCacheStrategy(INameCacheStrategy strategy){};\r
+ @Override\r
public INameCacheStrategy getCacheStrategy(){return null;};\r
+ @Override\r
public NomenclaturalCode getNomenclaturalCode(){return null;};\r
}\r
\r
\r
package eu.etaxonomy.cdm.model.taxon;\r
\r
-import static org.junit.Assert.*;\r
-\r
import java.util.ArrayList;\r
import java.util.Calendar;\r
import java.util.Collections;\r
import java.util.Calendar;\r
import java.util.Set;\r
\r
-import javax.activation.MimeType;\r
-\r
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.model.agent.Agent;\r
BGBM BDI Projects / cdmlib.git / commitdiff