Revision b9a0d300
Added by Lorna Morris over 12 years ago
| eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/store/TermStore.java | ||
|---|---|---|
| 11 | 11 |
package eu.etaxonomy.taxeditor.store; |
| 12 | 12 |
|
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import java.util.ArrayList; |
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import java.util.Arrays; |
|
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import java.util.Collections; |
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import java.util.Comparator; |
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import java.util.HashSet; |
|
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import java.util.List; |
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import java.util.Set; |
|
| 17 | 20 |
|
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import eu.etaxonomy.cdm.api.service.ITermService; |
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import eu.etaxonomy.cdm.api.service.IVocabularyService; |
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
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import eu.etaxonomy.cdm.model.common.AnnotationType; |
|
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.ExtensionType; |
|
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import eu.etaxonomy.cdm.model.common.Language; |
|
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.OrderedTermBase; |
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
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import eu.etaxonomy.cdm.model.common.TermVocabulary; |
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import eu.etaxonomy.cdm.model.common.VocabularyEnum; |
|
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import eu.etaxonomy.cdm.model.description.AbsenceTerm; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.MeasurementUnit; |
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import eu.etaxonomy.cdm.model.description.Modifier; |
|
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; |
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import eu.etaxonomy.cdm.model.description.PresenceTerm; |
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import eu.etaxonomy.cdm.model.description.Scope; |
|
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import eu.etaxonomy.cdm.model.description.Stage; |
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import eu.etaxonomy.cdm.model.description.State; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
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import eu.etaxonomy.cdm.model.location.NamedAreaType; |
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import eu.etaxonomy.cdm.model.location.ReferenceSystem; |
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import eu.etaxonomy.cdm.model.media.RightsTerm; |
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import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
|
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.occurrence.DeterminationModifier; |
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import eu.etaxonomy.cdm.model.occurrence.PreservationMethod; |
|
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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import eu.etaxonomy.taxeditor.model.TaxonRelationshipTypeInverseContainer; |
|
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import eu.etaxonomy.taxeditor.preference.PreferencesUtil; |
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|
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/** |
| ... | ... | |
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* @version 1.0 |
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*/ |
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public class TermStore {
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|
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/** |
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* <p>getSpecimenTypeDesignationStatus</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationStatus() {
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return getTerms(SpecimenTypeDesignationStatus.class); |
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} |
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/** |
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* <p>getNameTypeDesignationStatus</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<NameTypeDesignationStatus> getNameTypeDesignationStatus() {
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return getTerms(NameTypeDesignationStatus.class); |
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} |
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|
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/** |
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* <p>getNamedAreaTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<NamedAreaType> getNamedAreaTypes(){
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return getTerms(NamedAreaType.class); |
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} |
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|
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/** |
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* <p>getAnnotationTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<AnnotationType> getAnnotationTypes(){
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return getTerms(AnnotationType.class); |
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} |
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|
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/** |
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* <p>getTaxonRelationshipTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<TaxonRelationshipType> getTaxonRelationshipTypes(){
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return getTerms(TaxonRelationshipType.class); |
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public static <TERM extends DefinedTermBase> List<TERM> getTerms(Class<TERM> clazz){
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return getTerms(clazz, null, true); |
|
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} |
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|
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/** |
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* <p>getLanguages</p> |
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* |
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* @return a {@link java.util.List} object.
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* Returns a list of terms of the given type currently available in the system. |
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* If <code>filtered</code> is set to <code>true</code>, all terms for certain types will be |
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* gathered from edge cases. |
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* |
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* @param clazz |
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* @param comparator |
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* @param filtered Will filter out some results |
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* @return |
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*/ |
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public static List<Language> getLanguages(){
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return getTerms(Language.class); |
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} |
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|
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/** |
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* <p>getFeatures</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<Feature> getFeatures() {
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List<Feature> features = getTerms(Feature.class); |
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features.remove(Feature.IMAGE()); |
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return features; |
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} |
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/** |
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* <p>getNameRelationshipTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<NameRelationshipType> getNameRelationshipTypes() {
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return getTerms(NameRelationshipType.class); |
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} |
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|
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/** |
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* <p>getNomenclaturalStatusTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<NomenclaturalStatusType> getNomenclaturalStatusTypes(){
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return getTerms(NomenclaturalStatusType.class); |
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} |
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|
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public static <TERM extends DefinedTermBase> List<TERM> getTerms(Class<TERM> clazz, Comparator<TERM> comparator, boolean filtered){
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List<TERM> terms = new ArrayList<TERM>(); |
|
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/** |
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* <p>getNonTechnicalMarkerTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<MarkerType> getNonTechnicalMarkerTypes() {
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List<MarkerType> nonTechnicalMarkerTypes = new ArrayList<MarkerType>(); |
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List<MarkerType> markerTypes = getTerms(MarkerType.class); |
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for (Object type : markerTypes) {
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if (((MarkerType) type).isTechnical() == false) {
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nonTechnicalMarkerTypes.add((MarkerType) type); |
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} |
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ITermStoreEdgeCase<TERM> edgeCase = getEdgeCase(clazz); |
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if(filtered && edgeCase != null){
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terms = edgeCase.getTerms(); |
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}else{
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terms = getTermsFromService(clazz, comparator); |
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} |
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return nonTechnicalMarkerTypes; |
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} |
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/** |
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* <p>getExtensionTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<ExtensionType> getExtensionTypes() {
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return getTerms(ExtensionType.class); |
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} |
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|
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/** |
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* <p>getRightsTypes</p> |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<RightsTerm> getRightsTypes() {
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return getTerms(RightsTerm.class); |
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return terms; |
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|
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} |
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|
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/** |
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* Retrieve all ranks from data store. |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<Rank> getRanks(){
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if(PreferencesUtil.getSortRanksHierarchichally()){
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return getTerms(Rank.class, new Comparator<Rank>(){
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|
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private static <T extends DefinedTermBase> List<T> getTermsFromService(Class<T> termClass, Comparator<T> comparator){
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if (comparator == null){
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comparator = new Comparator<T>() {
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@Override |
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public int compare(Rank o1, Rank o2) {
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return o1.compareTo(o2); |
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public int compare(T o1, T o2) {
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String label1 = o1.getLabel(CdmStore.getDefaultLanguage()) != null ? o1.getLabel(CdmStore.getDefaultLanguage()) : o1.getTitleCache(); |
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String label2 = o2.getLabel(CdmStore.getDefaultLanguage()) != null ? o2.getLabel(CdmStore.getDefaultLanguage()) : o2.getTitleCache(); |
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return label1.compareTo(label2); |
|
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} |
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|
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}); |
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}else{
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return getTerms(Rank.class); |
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}; |
|
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} |
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|
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List<T> terms = CdmStore.getService(ITermService.class).listByTermClass(termClass, null, null, null, null); |
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Collections.sort(terms, comparator); |
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return terms; |
|
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} |
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|
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// /** |
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// * <p>getFeatures</p> |
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// * |
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// * @return a {@link java.util.List} object.
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// */ |
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// public static List<Feature> getFeatures() {
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// List<Feature> features = getTerms(Feature.class); |
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// features.remove(Feature.IMAGE()); |
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// return features; |
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// |
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// } |
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// |
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// |
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// /** |
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// * <p>getNonTechnicalMarkerTypes</p> |
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// * |
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// * @return a {@link java.util.List} object.
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// */ |
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// public static List<MarkerType> getNonTechnicalMarkerTypes() {
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// List<MarkerType> nonTechnicalMarkerTypes = new ArrayList<MarkerType>(); |
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// List<MarkerType> markerTypes = getTerms(MarkerType.class); |
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// |
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// for (Object type : markerTypes) {
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// if (((MarkerType) type).isTechnical() == false) {
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// nonTechnicalMarkerTypes.add((MarkerType) type); |
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// } |
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// } |
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// |
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// return nonTechnicalMarkerTypes; |
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// } |
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// |
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// /** |
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// * Retrieve all ranks from data store. |
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// * |
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// * @return a {@link java.util.List} object.
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// */ |
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// public static List<Rank> getRanks(){
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// if(PreferencesUtil.getSortRanksHierarchichally()){
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// return getTerms(Rank.class, new Comparator<Rank>(){
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// |
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// @Override |
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// public int compare(Rank o1, Rank o2) {
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// return o1.compareTo(o2); |
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// } |
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// |
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// }); |
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// }else{
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// return getTerms(Rank.class); |
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// } |
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// } |
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// |
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// |
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// /** |
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// * Retrieve all presence and absence terms from data store. |
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// * |
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// * @return a {@link java.util.List} object.
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// */ |
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// public static List<PresenceAbsenceTermBase> getPresenceAbsenceTerms() {
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// List presenceAbsenceTerms = getTerms(PresenceTerm.class); |
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// presenceAbsenceTerms.addAll(getTerms(AbsenceTerm.class)); |
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// |
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// return presenceAbsenceTerms; |
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// } |
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|
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/** |
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* Retrieve all presence and absence terms from data store. |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<PresenceAbsenceTermBase> getPresenceAbsenceTerms() {
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List presenceAbsenceTerms = getTerms(PresenceTerm.class); |
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presenceAbsenceTerms.addAll(getTerms(AbsenceTerm.class)); |
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return presenceAbsenceTerms; |
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} |
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|
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/** |
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* Retrieve all stages from data store. |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<Stage> getStages(){
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return getTerms(Stage.class); |
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} |
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|
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/** |
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* Retrieve all states from data store. |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<State> getStates() {
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return getTerms(State.class); |
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} |
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|
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/** |
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* Retrieve all preservation methods from data store. |
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* |
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* @return a {@link java.util.List} object.
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*/ |
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public static List<PreservationMethod> getPreservationMethods(){
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return getTerms(PreservationMethod.class); |
|
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} |
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|
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|
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|
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/** |
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* <p>getMeasurementUnits</p> |
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* |
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* @return a {@link java.util.List} object.
|
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*/ |
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public static List<MeasurementUnit> getMeasurementUnits() {
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return getTerms(MeasurementUnit.class); |
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} |
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|
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|
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/** |
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* <p>getModifiers</p> |
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* |
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* @return a {@link java.util.List} object.
|
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*/ |
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public static List<Modifier> getModifiers() {
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return getTerms(Modifier.class); |
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} |
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|
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|
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/** |
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* <p>getStatisticalMeasures</p> |
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* |
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* @return a {@link java.util.List} object.
|
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*/ |
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public static List<StatisticalMeasure> getStatisticalMeasures() {
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return getTerms(StatisticalMeasure.class); |
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} |
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|
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/** |
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* <p>getScopes</p> |
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* |
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* @return a {@link java.util.List} object.
|
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*/ |
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public static List<Scope> getScopes() {
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return getTerms(Scope.class); |
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} |
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|
|
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/** |
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* <p>getDeterminationModifiers</p> |
|
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* |
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* @return a {@link java.util.List} object.
|
|
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*/ |
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public static List<DeterminationModifier> getDeterminationModifiers() {
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return getTerms(DeterminationModifier.class); |
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} |
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|
|
| 298 |
/** |
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* <p>getReferenceSystems</p> |
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* |
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* @return a {@link java.util.List} object.
|
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| 302 |
*/ |
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public static List<ReferenceSystem> getReferenceSystems() {
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return getTerms(ReferenceSystem.class); |
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} |
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|
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| 307 |
/** |
|
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************* save methods ***************************** |
|
| 309 |
* |
|
| 310 | 156 |
* @param term a {@link eu.etaxonomy.cdm.model.common.DefinedTermBase} object.
|
| 311 | 157 |
*/ |
| 312 | 158 |
public static void saveTerm(DefinedTermBase term){
|
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getTermService().saveOrUpdate(term);
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CdmStore.getService(ITermService.class).saveOrUpdate(term);
|
|
| 314 | 160 |
} |
| 315 | 161 |
|
| 316 | 162 |
/** |
| ... | ... | |
| 319 | 165 |
* @param selected a {@link eu.etaxonomy.cdm.model.common.DefinedTermBase} object.
|
| 320 | 166 |
*/ |
| 321 | 167 |
public static void delete(DefinedTermBase selected) {
|
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getTermService().delete(selected);
|
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CdmStore.getService(ITermService.class).delete(selected);
|
|
| 323 | 169 |
} |
| 324 | 170 |
|
| 325 | 171 |
/** |
| ... | ... | |
| 328 | 174 |
* @param term a {@link eu.etaxonomy.cdm.model.common.DefinedTermBase} object.
|
| 329 | 175 |
*/ |
| 330 | 176 |
public static void updateVocabulary(DefinedTermBase term) {
|
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getTermService().saveOrUpdate(term);
|
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CdmStore.getService(ITermService.class).saveOrUpdate(term);
|
|
| 332 | 178 |
} |
| 333 | 179 |
|
| 180 |
private static Set<ITermStoreEdgeCase<? extends DefinedTermBase>> termStoreEdgeCases = new HashSet<ITermStoreEdgeCase<? extends DefinedTermBase>>(); |
|
| 334 | 181 |
|
| 335 |
|
|
| 336 |
/*************** internal methods **************************/ |
|
| 337 |
|
|
| 338 |
private static Language getDefaultLanguage(){
|
|
| 339 |
return CdmStore.getDefaultLanguage(); |
|
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} |
|
| 341 |
|
|
| 342 |
private static OrderedTermVocabulary<? extends OrderedTermBase> getOrderedTermVocabulary(VocabularyEnum vocabularyType){
|
|
| 343 |
TermVocabulary<DefinedTermBase> vocabulary = getTermVocabulary(vocabularyType); |
|
| 344 |
return HibernateProxyHelper.deproxy(vocabulary, OrderedTermVocabulary.class); |
|
| 182 |
static {
|
|
| 183 |
termStoreEdgeCases.add(new ITermStoreEdgeCase<Feature>() {
|
|
| 184 |
|
|
| 185 |
@Override |
|
| 186 |
public Class<Feature> getTermClass() {
|
|
| 187 |
return Feature.class; |
|
| 188 |
} |
|
| 189 |
|
|
| 190 |
@Override |
|
| 191 |
public List<Feature> getTerms() {
|
|
| 192 |
List<Feature> features = TermStore.getTermsFromService(Feature.class, null); |
|
| 193 |
features.remove(Feature.IMAGE()); |
|
| 194 |
return features; |
|
| 195 |
} |
|
| 196 |
}); |
|
| 197 |
termStoreEdgeCases.add(new ITermStoreEdgeCase<MarkerType>(){
|
|
| 198 |
|
|
| 199 |
@Override |
|
| 200 |
public Class<MarkerType> getTermClass() {
|
|
| 201 |
return MarkerType.class; |
|
| 202 |
} |
|
| 203 |
|
|
| 204 |
@Override |
|
| 205 |
public List<MarkerType> getTerms() {
|
|
| 206 |
// filter out non technical markers |
|
| 207 |
List<MarkerType> nonTechnicalMarkerTypes = new ArrayList<MarkerType>(); |
|
| 208 |
List<MarkerType> markerTypes = TermStore.getTermsFromService(MarkerType.class, null); |
|
| 209 |
|
|
| 210 |
for (Object type : markerTypes) {
|
|
| 211 |
if (((MarkerType) type).isTechnical() == false) {
|
|
| 212 |
nonTechnicalMarkerTypes.add((MarkerType) type); |
|
| 213 |
} |
|
| 214 |
} |
|
| 215 |
|
|
| 216 |
return nonTechnicalMarkerTypes; |
|
| 217 |
} |
|
| 218 |
|
|
| 219 |
}); |
|
| 220 |
termStoreEdgeCases.add(new ITermStoreEdgeCase<Rank>() {
|
|
| 221 |
|
|
| 222 |
@Override |
|
| 223 |
public Class<Rank> getTermClass() {
|
|
| 224 |
return Rank.class; |
|
| 225 |
} |
|
| 226 |
|
|
| 227 |
@Override |
|
| 228 |
public List<Rank> getTerms() {
|
|
| 229 |
if(PreferencesUtil.getSortRanksHierarchichally()){
|
|
| 230 |
return TermStore.getTermsFromService(Rank.class, new Comparator<Rank>(){
|
|
| 231 |
|
|
| 232 |
@Override |
|
| 233 |
public int compare(Rank o1, Rank o2) {
|
|
| 234 |
return o1.compareTo(o2); |
|
| 235 |
} |
|
| 236 |
|
|
| 237 |
}); |
|
| 238 |
}else{
|
|
| 239 |
return TermStore.getTermsFromService(Rank.class, null); |
|
| 240 |
} |
|
| 241 |
} |
|
| 242 |
|
|
| 243 |
}); |
|
| 244 |
termStoreEdgeCases.add(new ITermStoreEdgeCase<PresenceAbsenceTermBase>() {
|
|
| 245 |
|
|
| 246 |
@Override |
|
| 247 |
public Class<PresenceAbsenceTermBase> getTermClass() {
|
|
| 248 |
return PresenceAbsenceTermBase.class; |
|
| 249 |
} |
|
| 250 |
|
|
| 251 |
@Override |
|
| 252 |
public List<PresenceAbsenceTermBase> getTerms() {
|
|
| 253 |
List presenceAbsenceTerms = TermStore.getTermsFromService(PresenceTerm.class, null); |
|
| 254 |
presenceAbsenceTerms.addAll(TermStore.getTermsFromService(AbsenceTerm.class, null)); |
|
| 255 |
|
|
| 256 |
return presenceAbsenceTerms; |
|
| 257 |
} |
|
| 258 |
}); |
|
| 259 |
termStoreEdgeCases.add(new ITermStoreEdgeCase<TaxonRelationshipTypeInverseContainer>() {
|
|
| 260 |
|
|
| 261 |
@Override |
|
| 262 |
public Class<TaxonRelationshipTypeInverseContainer> getTermClass() {
|
|
| 263 |
return TaxonRelationshipTypeInverseContainer.class; |
|
| 264 |
} |
|
| 265 |
|
|
| 266 |
@Override |
|
| 267 |
public List<TaxonRelationshipTypeInverseContainer> getTerms() {
|
|
| 268 |
List<TaxonRelationshipType> excludeTaxonRelationshipTypes = Arrays.asList(new TaxonRelationshipType[]{
|
|
| 269 |
TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), |
|
| 270 |
TaxonRelationshipType.MISAPPLIED_NAME_FOR(), |
|
| 271 |
TaxonRelationshipType.ALL_RELATIONSHIPS() |
|
| 272 |
}); |
|
| 273 |
|
|
| 274 |
List<TaxonRelationshipTypeInverseContainer> relationshipTypeInverseContainers = new ArrayList<TaxonRelationshipTypeInverseContainer>(); |
|
| 275 |
|
|
| 276 |
List<TaxonRelationshipType> relationshipTypes = TermStore.getTerms(TaxonRelationshipType.class); |
|
| 277 |
|
|
| 278 |
relationshipTypes.removeAll(excludeTaxonRelationshipTypes); |
|
| 279 |
|
|
| 280 |
for (TaxonRelationshipType relationshipType : relationshipTypes){
|
|
| 281 |
if(!relationshipType.isSymmetric()){
|
|
| 282 |
TaxonRelationshipTypeInverseContainer inverseContainer = new TaxonRelationshipTypeInverseContainer(relationshipType, true); |
|
| 283 |
relationshipTypeInverseContainers.add(inverseContainer); |
|
| 284 |
} |
|
| 285 |
TaxonRelationshipTypeInverseContainer container = new TaxonRelationshipTypeInverseContainer(relationshipType, false); |
|
| 286 |
relationshipTypeInverseContainers.add(container); |
|
| 287 |
} |
|
| 288 |
|
|
| 289 |
return relationshipTypeInverseContainers; |
|
| 290 |
} |
|
| 291 |
}); |
|
| 345 | 292 |
} |
| 346 | 293 |
|
| 347 |
/** |
|
| 348 |
* <p>getTermVocabulary</p> |
|
| 349 |
* |
|
| 350 |
* @param vocabularyType a {@link eu.etaxonomy.cdm.model.common.VocabularyEnum} object.
|
|
| 351 |
* @return a {@link eu.etaxonomy.cdm.model.common.TermVocabulary} object.
|
|
| 352 |
*/ |
|
| 353 |
public static TermVocabulary<DefinedTermBase> getTermVocabulary(VocabularyEnum vocabularyType){
|
|
| 294 |
private static <T extends DefinedTermBase> ITermStoreEdgeCase<T> getEdgeCase(Class<T> termClass) {
|
|
| 354 | 295 |
|
| 355 |
return CdmStore.getService(IVocabularyService.class).getVocabulary(vocabularyType); |
|
| 356 |
} |
|
| 357 |
|
|
| 358 |
private static <TERM extends DefinedTermBase> List<TERM> getTerms(Class<TERM> clazz){
|
|
| 359 |
Comparator<TERM> comparator = new Comparator<TERM>() {
|
|
| 360 |
@Override |
|
| 361 |
public int compare(TERM o1, TERM o2) {
|
|
| 362 |
String label1 = o1.getLabel(getDefaultLanguage()) != null ? o1.getLabel(getDefaultLanguage()) : o1.getTitleCache(); |
|
| 363 |
String label2 = o2.getLabel(getDefaultLanguage()) != null ? o2.getLabel(getDefaultLanguage()) : o2.getTitleCache(); |
|
| 364 |
return label1.compareTo(label2); |
|
| 296 |
for (ITermStoreEdgeCase termStoreEdgeCase : termStoreEdgeCases){
|
|
| 297 |
if (termStoreEdgeCase.getTermClass().equals(termClass)){
|
|
| 298 |
return termStoreEdgeCase; |
|
| 365 | 299 |
} |
| 366 |
};
|
|
| 300 |
} |
|
| 367 | 301 |
|
| 368 |
return getTerms(clazz, comparator);
|
|
| 302 |
return null;
|
|
| 369 | 303 |
} |
| 370 | 304 |
|
| 371 |
|
|
| 372 |
private static <TERM extends DefinedTermBase> List<TERM> getTerms(Class<TERM> clazz, Comparator<TERM> comparator){
|
|
| 305 |
private interface ITermStoreEdgeCase<TERM> {
|
|
| 373 | 306 |
|
| 307 |
public abstract Class<TERM> getTermClass(); |
|
| 374 | 308 |
|
| 375 |
List<TERM> terms = new ArrayList<TERM>(); |
|
| 376 |
if(getTermService() != null){
|
|
| 377 |
terms = getTermService().listByTermClass(clazz, null, null, null, null); |
|
| 309 |
public abstract List<TERM> getTerms(); |
|
| 378 | 310 |
|
| 379 |
Collections.sort(terms, comparator); |
|
| 380 |
} |
|
| 381 |
|
|
| 382 |
return terms; |
|
| 383 |
|
|
| 384 |
} |
|
| 385 |
|
|
| 386 |
private static ITermService getTermService(){
|
|
| 387 |
return CdmStore.getService(ITermService.class); |
|
| 388 | 311 |
} |
| 389 | 312 |
} |
Also available in: Unified diff
Committing changes to definedtermeditor after merge from branch