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/**
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* Copyright (C) 2017 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.vaadin.util.converter;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.Map;
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import java.util.Optional;
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import java.util.Set;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.vaadin.model.EntityReference;
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import eu.etaxonomy.cdm.vaadin.model.TypedEntityReference;
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import eu.etaxonomy.cdm.vaadin.view.registration.RegistrationValidationException;
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/**
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* Converts a collection of TypeDesignations, which should belong to the
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* same name of course, into a string representation.
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*
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* Order of TypeDesignations in the resulting string:
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* Type, Holotype, Lectotype, Epitypes
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* @author a.kohlbecker
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* @since Mar 10, 2017
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*
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*/
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public class TypeDesignationConverter {
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private static final String TYPE_STATUS_SEPARATOR = "; ";
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private static final String TYPE_SEPARATOR = "; ";
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private static final String TYPE_DESIGNATION_SEPARATOR = ", ";
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private Collection<TypeDesignationBase> typeDesignations;
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/**
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* Groups the EntityReferences for each of the TypeDesignations by the according TypeDesignationStatus.
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* The TypeDesignationStatusBase keys are already ordered by the term order defined in the vocabulary.
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*/
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private LinkedHashMap<TypedEntityReference, TypeDesignationWorkingSet> orderedByTypesByBaseEntity;
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private EntityReference typifiedName;
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private String finalString = null;
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/**
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* @param taxonName
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* @throws RegistrationValidationException
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*
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*/
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public TypeDesignationConverter(CdmBase containgEntity, Collection<TypeDesignationBase> typeDesignations) throws RegistrationValidationException {
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this.typeDesignations = typeDesignations;
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Map<TypedEntityReference, TypeDesignationWorkingSet> byBaseEntityByTypeStatus = new HashMap<>();
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typeDesignations.forEach(td -> mapTypeDesignation(containgEntity, byBaseEntityByTypeStatus, td));
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orderedByTypesByBaseEntity = orderByTypeByBaseEntity(byBaseEntityByTypeStatus);
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this.typifiedName = findTypifiedName();
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}
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private void mapTypeDesignation(CdmBase containgEntity, Map<TypedEntityReference, TypeDesignationWorkingSet> byBaseEntityByTypeStatus,
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TypeDesignationBase<?> td){
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TypeDesignationStatusBase<?> status = td.getTypeStatus();
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final TypedEntityReference baseEntityReference = baseEntityReference(td);
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EntityReference typeDesignationEntityReference = new EntityReference(td.getId(), stringify(td));
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TypeDesignationWorkingSet typedesignationWorkingSet;
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if(!byBaseEntityByTypeStatus.containsKey(baseEntityReference)){
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TypedEntityReference containigEntityReference = new TypedEntityReference(containgEntity.getClass(), containgEntity.getId(), containgEntity.toString());
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byBaseEntityByTypeStatus.put(baseEntityReference, new TypeDesignationWorkingSet(containigEntityReference, baseEntityReference));
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}
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typedesignationWorkingSet = byBaseEntityByTypeStatus.get(baseEntityReference);
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typedesignationWorkingSet.insert(status, typeDesignationEntityReference);
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}
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/**
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* @param td
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* @return
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*/
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protected TypedEntityReference baseEntityReference(TypeDesignationBase<?> td) {
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CdmBase baseEntity = null;
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String label = "";
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if(td instanceof SpecimenTypeDesignation){
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SpecimenTypeDesignation std = (SpecimenTypeDesignation) td;
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FieldUnit fu = findFieldUnit(std);
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if(fu != null){
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baseEntity = fu;
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label = fu.getTitleCache();
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} else if(((SpecimenTypeDesignation) td).getTypeSpecimen() != null){
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baseEntity = ((SpecimenTypeDesignation) td).getTypeSpecimen();
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label = ""; // empty label to avoid repeating the DerivedUnit details
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}
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} else if(td instanceof NameTypeDesignation){
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baseEntity = ((NameTypeDesignation)td).getTypeName();
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label = "";
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}
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if(baseEntity == null) {
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baseEntity = td;
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label = "INCOMPLETE DATA";
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}
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TypedEntityReference baseEntityReference = new TypedEntityReference(baseEntity.getClass(), baseEntity.getId(), label);
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return baseEntityReference;
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}
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private LinkedHashMap<TypedEntityReference, TypeDesignationWorkingSet> orderByTypeByBaseEntity(
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Map<TypedEntityReference, TypeDesignationWorkingSet> stringsByTypeByBaseEntity){
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// order the FieldUnit TypeName keys
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List<TypedEntityReference> baseEntityKeyList = new LinkedList<>(stringsByTypeByBaseEntity.keySet());
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Collections.sort(baseEntityKeyList, new Comparator<TypedEntityReference>(){
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@Override
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public int compare(TypedEntityReference o1, TypedEntityReference o2) {
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if(!o1.getType().equals(o2.getType())) {
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return o1.getType().equals(FieldUnit.class) ? -1 : 1;
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}
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return o1.getLabel().compareTo(o2.getLabel());
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}});
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// new LinkedHashMap for the ordered FieldUnitOrTypeName keys
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LinkedHashMap<TypedEntityReference, TypeDesignationWorkingSet> stringsOrderedbyBaseEntityOrderdByType = new LinkedHashMap<>(stringsByTypeByBaseEntity.size());
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for(TypedEntityReference baseEntityRef : baseEntityKeyList){
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TypeDesignationWorkingSet typeDesignationWorkingSet = stringsByTypeByBaseEntity.get(baseEntityRef);
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// order the TypeDesignationStatusBase keys
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List<TypeDesignationStatusBase<?>> keyList = new LinkedList<>(typeDesignationWorkingSet.keySet());
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Collections.sort(keyList, new Comparator<TypeDesignationStatusBase>() {
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@Override
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public int compare(TypeDesignationStatusBase o1, TypeDesignationStatusBase o2) {
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// fix inverted order of cdm terms by -1*
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return -1 * o1.compareTo(o2);
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}
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});
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// new LinkedHashMap for the ordered TypeDesignationStatusBase keys
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TypeDesignationWorkingSet orderedStringsByOrderedTypes = new TypeDesignationWorkingSet(typeDesignationWorkingSet.getContainigEntityReference(), baseEntityRef);
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keyList.forEach(key -> orderedStringsByOrderedTypes.put(key, typeDesignationWorkingSet.get(key)));
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stringsOrderedbyBaseEntityOrderdByType.put(baseEntityRef, orderedStringsByOrderedTypes);
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}
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return stringsOrderedbyBaseEntityOrderdByType;
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}
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/*
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private LinkedHashMap<TypedEntityReference, LinkedHashMap<String, Collection<EntityReference>>> buildOrderedRepresentations(){
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orderedStringsByOrderedTypes.keySet().forEach(
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key -> orderedRepresentations.put(
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getTypeDesignationStytusLabel(key),
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orderedStringsByOrderedTypes.get(key))
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);
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return orderedRepresentations;
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}
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*/
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public TypeDesignationConverter buildString(){
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if(finalString == null){
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finalString = "";
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if(getTypifiedNameCache() != null){
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finalString += getTypifiedNameCache() + " ";
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}
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int typeCount = 0;
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for(TypedEntityReference baseEntityRef : orderedByTypesByBaseEntity.keySet()) {
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StringBuilder sb = new StringBuilder();
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if(typeCount++ > 0){
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sb.append(TYPE_SEPARATOR);
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}
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boolean isNameTypeDesignation = false;
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if(SpecimenOrObservationBase.class.isAssignableFrom(baseEntityRef.getType())){
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sb.append("Type: ");
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} else {
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sb.append("NameType: ");
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isNameTypeDesignation = true;
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}
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if(!baseEntityRef.getLabel().isEmpty()){
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sb.append(baseEntityRef.getLabel()).append(" ");
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}
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TypeDesignationWorkingSet typeDesignationWorkingSet = orderedByTypesByBaseEntity.get(baseEntityRef);
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if(!isNameTypeDesignation ){
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sb.append("(");
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}
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int typeStatusCount = 0;
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for(TypeDesignationStatusBase<?> typeStatus : typeDesignationWorkingSet.keySet()) {
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if(typeStatusCount++ > 0){
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sb.append(TYPE_STATUS_SEPARATOR);
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}
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boolean isPlural = typeDesignationWorkingSet.get(typeStatus).size() > 1;
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sb.append(typeStatus.getLabel());
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if(isPlural){
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sb.append("s: ");
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} else {
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sb.append(", ");
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}
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int typeDesignationCount = 0;
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for(EntityReference typeDesignationEntityReference : typeDesignationWorkingSet.get(typeStatus)) {
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if(typeDesignationCount++ > 0){
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sb.append(TYPE_DESIGNATION_SEPARATOR);
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}
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sb.append(typeDesignationEntityReference.getLabel());
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}
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}
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if(!isNameTypeDesignation ){
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sb.append(")");
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}
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typeDesignationWorkingSet.setRepresentation(sb.toString());
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finalString += typeDesignationWorkingSet.getRepresentation();
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}
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}
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return this;
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}
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/**
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* FIXME use the validation framework validators and to store the validation problems!!!
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*
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* @return
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* @throws RegistrationValidationException
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*/
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private EntityReference findTypifiedName() throws RegistrationValidationException {
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List<String> problems = new ArrayList<>();
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TaxonName typifiedName = null;
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for(TypeDesignationBase<?> typeDesignation : typeDesignations){
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typeDesignation.getTypifiedNames();
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if(typeDesignation.getTypifiedNames().isEmpty()){
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//TODO instead throw RegistrationValidationException()
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problems.add("Missing typifiedName in " + typeDesignation.toString());
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continue;
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}
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if(typeDesignation.getTypifiedNames().size() > 1){
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//TODO instead throw RegistrationValidationException()
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problems.add("Multiple typifiedName in " + typeDesignation.toString());
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continue;
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}
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if(typifiedName == null){
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// remember
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typifiedName = typeDesignation.getTypifiedNames().iterator().next();
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} else {
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// compare
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TaxonName otherTypifiedName = typeDesignation.getTypifiedNames().iterator().next();
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if(typifiedName.getId() != otherTypifiedName.getId()){
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//TODO instead throw RegistrationValidationException()
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problems.add("Multiple typifiedName in " + typeDesignation.toString());
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}
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}
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}
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if(!problems.isEmpty()){
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// FIXME use the validation framework
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throw new RegistrationValidationException("Inconsistent type designations", problems);
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}
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if(typifiedName != null){
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return new EntityReference(typifiedName.getId(), typifiedName.getTitleCache());
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}
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return null;
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}
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/**
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* @return the title cache of the typifying name or <code>null</code>
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*/
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public String getTypifiedNameCache() {
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if(typifiedName != null){
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return typifiedName.getLabel();
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}
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return null;
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}
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/**
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* @return the title cache of the typifying name or <code>null</code>
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*/
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public EntityReference getTypifiedName() {
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return typifiedName;
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}
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/**
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* @return
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*/
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public Collection<TypeDesignationBase> getTypeDesignations() {
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return typeDesignations;
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}
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public LinkedHashMap<TypedEntityReference, TypeDesignationWorkingSet> getOrderdTypeDesignationWorkingSets() {
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return orderedByTypesByBaseEntity;
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}
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/**
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* @param key
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* @return
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*/
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protected String getTypeDesignationStytusLabel(TypeDesignationStatusBase<?> key) {
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String typeLable;
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if(key.equals( SpecimenTypeDesignationStatus.TYPE())){
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typeLable = "Type";
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} else {
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typeLable = key.getPreferredRepresentation(Language.DEFAULT()).getLabel();
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}
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return typeLable;
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}
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/**
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* @param td
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* @return
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*/
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private String stringify(TypeDesignationBase td) {
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if(td instanceof NameTypeDesignation){
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return stringify((NameTypeDesignation)td);
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} else {
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return stringify((SpecimenTypeDesignation)td, false);
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}
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}
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/**
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* @param td
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* @return
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*/
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protected String stringify(NameTypeDesignation td) {
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StringBuffer sb = new StringBuffer();
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if(td.getTypeName() != null){
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sb.append(td.getTypeName().getTitleCache());
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}
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if(td.getCitation() != null){
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sb.append(" ").append(td.getCitation().getTitleCache());
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if(td.getCitationMicroReference() != null){
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sb.append(":").append(td.getCitationMicroReference());
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}
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}
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if(td.isNotDesignated()){
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sb.append(" not designated");
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}
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if(td.isRejectedType()){
|
|
377
|
sb.append(" rejected");
|
|
378
|
}
|
|
379
|
if(td.isConservedType()){
|
|
380
|
sb.append(" conserved");
|
|
381
|
}
|
|
382
|
return sb.toString();
|
|
383
|
}
|
|
384
|
|
|
385
|
/**
|
|
386
|
* @param td
|
|
387
|
* @return
|
|
388
|
*/
|
|
389
|
private String stringify(SpecimenTypeDesignation td, boolean useFullTitleCache) {
|
|
390
|
String result = "";
|
|
391
|
|
|
392
|
if(useFullTitleCache){
|
|
393
|
if(td.getTypeSpecimen() != null){
|
|
394
|
String nameTitleCache = td.getTypeSpecimen().getTitleCache();
|
|
395
|
if(getTypifiedNameCache() != null){
|
|
396
|
nameTitleCache = nameTitleCache.replace(getTypifiedNameCache(), "");
|
|
397
|
}
|
|
398
|
result += nameTitleCache;
|
|
399
|
}
|
|
400
|
} else {
|
|
401
|
if(td.getTypeSpecimen() != null){
|
|
402
|
DerivedUnit du = td.getTypeSpecimen();
|
|
403
|
if(du.isProtectedTitleCache()){
|
|
404
|
result += du.getTitleCache();
|
|
405
|
} else {
|
|
406
|
DerivedUnitFacadeCacheStrategy cacheStrategy = new DerivedUnitFacadeCacheStrategy();
|
|
407
|
result += cacheStrategy.getTitleCache(du, true);
|
|
408
|
}
|
|
409
|
}
|
|
410
|
}
|
|
411
|
|
|
412
|
if(td.getCitation() != null){
|
|
413
|
result += " " + td.getCitation().getTitleCache();
|
|
414
|
if(td.getCitationMicroReference() != null){
|
|
415
|
result += " :" + td.getCitationMicroReference();
|
|
416
|
}
|
|
417
|
}
|
|
418
|
if(td.isNotDesignated()){
|
|
419
|
result += " not designated";
|
|
420
|
}
|
|
421
|
|
|
422
|
return result;
|
|
423
|
}
|
|
424
|
|
|
425
|
/**
|
|
426
|
* @param td
|
|
427
|
* @return
|
|
428
|
* @deprecated
|
|
429
|
*/
|
|
430
|
@Deprecated
|
|
431
|
private FieldUnit findFieldUnit(SpecimenTypeDesignation td) {
|
|
432
|
|
|
433
|
DerivedUnit du = td.getTypeSpecimen();
|
|
434
|
return findFieldUnit(du);
|
|
435
|
}
|
|
436
|
|
|
437
|
private FieldUnit findFieldUnit(DerivedUnit du) {
|
|
438
|
|
|
439
|
if(du == null || du.getOriginals() == null){
|
|
440
|
return null;
|
|
441
|
}
|
|
442
|
@SuppressWarnings("rawtypes")
|
|
443
|
Set<SpecimenOrObservationBase> originals = du.getDerivedFrom().getOriginals();
|
|
444
|
@SuppressWarnings("rawtypes")
|
|
445
|
Optional<SpecimenOrObservationBase> fieldUnit = originals.stream()
|
|
446
|
.filter(original -> original instanceof FieldUnit).findFirst();
|
|
447
|
if (fieldUnit.isPresent()) {
|
|
448
|
return (FieldUnit) fieldUnit.get();
|
|
449
|
} else {
|
|
450
|
for (@SuppressWarnings("rawtypes")
|
|
451
|
SpecimenOrObservationBase sob : originals) {
|
|
452
|
if (sob instanceof DerivedUnit) {
|
|
453
|
FieldUnit fu = findFieldUnit((DerivedUnit) sob);
|
|
454
|
if (fu != null) {
|
|
455
|
return fu;
|
|
456
|
}
|
|
457
|
}
|
|
458
|
}
|
|
459
|
}
|
|
460
|
|
|
461
|
return null;
|
|
462
|
}
|
|
463
|
|
|
464
|
public String print() {
|
|
465
|
return finalString;
|
|
466
|
}
|
|
467
|
|
|
468
|
/**
|
|
469
|
* Groups the EntityReferences for TypeDesignations by the according TypeDesignationStatus.
|
|
470
|
* The TypeDesignationStatusBase keys can be ordered by the term order defined in the vocabulary.
|
|
471
|
*/
|
|
472
|
public class TypeDesignationWorkingSet extends LinkedHashMap<TypeDesignationStatusBase<?>, Collection<EntityReference>> {
|
|
473
|
|
|
474
|
String workingSetRepresentation = null;
|
|
475
|
|
|
476
|
TypedEntityReference containigEntityReference;
|
|
477
|
|
|
478
|
TypedEntityReference baseEntityReference;
|
|
479
|
|
|
480
|
private static final long serialVersionUID = -1329007606500890729L;
|
|
481
|
|
|
482
|
/**
|
|
483
|
* @param baseEntityReference
|
|
484
|
*/
|
|
485
|
public TypeDesignationWorkingSet(TypedEntityReference containigEntityReference, TypedEntityReference baseEntityReference) {
|
|
486
|
this.containigEntityReference = containigEntityReference;
|
|
487
|
this.baseEntityReference = baseEntityReference;
|
|
488
|
}
|
|
489
|
|
|
490
|
public List<EntityReference> getTypeDesignations() {
|
|
491
|
List<EntityReference> typeDesignations = new ArrayList<>();
|
|
492
|
this.values().forEach(typeDesignationReferences -> typeDesignationReferences.forEach(td -> typeDesignations.add(td)));
|
|
493
|
return typeDesignations;
|
|
494
|
}
|
|
495
|
|
|
496
|
/**
|
|
497
|
* @param status
|
|
498
|
* @param typeDesignationEntityReference
|
|
499
|
*/
|
|
500
|
public void insert(TypeDesignationStatusBase<?> status, EntityReference typeDesignationEntityReference) {
|
|
501
|
|
|
502
|
if(status == null){
|
|
503
|
status = SpecimenTypeDesignationStatus.TYPE();
|
|
504
|
}
|
|
505
|
if(!containsKey(status)){
|
|
506
|
put(status, new ArrayList<EntityReference>());
|
|
507
|
}
|
|
508
|
get(status).add(typeDesignationEntityReference);
|
|
509
|
}
|
|
510
|
|
|
511
|
public String getRepresentation() {
|
|
512
|
return workingSetRepresentation;
|
|
513
|
}
|
|
514
|
|
|
515
|
public void setRepresentation(String representation){
|
|
516
|
this.workingSetRepresentation = representation;
|
|
517
|
}
|
|
518
|
|
|
519
|
/**
|
|
520
|
* A reference to the entity which is the common base entity for all TypeDesignations in this workingset.
|
|
521
|
* For a {@link SpecimenTypeDesignation} this is usually the {@link FieldUnit} if it is present. Otherwise it can also be
|
|
522
|
* a {@link DerivedUnit} or something else depending on the specific use case.
|
|
523
|
*
|
|
524
|
* @return the baseEntityReference
|
|
525
|
*/
|
|
526
|
public TypedEntityReference getBaseEntityReference() {
|
|
527
|
return baseEntityReference;
|
|
528
|
}
|
|
529
|
|
|
530
|
/**
|
|
531
|
* A reference to the entity which contains the TypeDesignations bundled in this working set.
|
|
532
|
* This can be for example a {@link TaxonName} or a {@link Registration} entity.
|
|
533
|
*
|
|
534
|
* @return the baseEntityReference
|
|
535
|
*/
|
|
536
|
public TypedEntityReference getContainigEntityReference() {
|
|
537
|
return containigEntityReference;
|
|
538
|
}
|
|
539
|
|
|
540
|
@Override
|
|
541
|
public String toString(){
|
|
542
|
if(workingSetRepresentation != null){
|
|
543
|
return workingSetRepresentation;
|
|
544
|
} else {
|
|
545
|
return super.toString();
|
|
546
|
}
|
|
547
|
}
|
|
548
|
|
|
549
|
}
|
|
550
|
|
|
551
|
}
|