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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 TypeDesignatinos 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, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> 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(Collection<TypeDesignationBase> typeDesignations) throws RegistrationValidationException {
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this.typeDesignations = typeDesignations;
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Map<TypedEntityReference, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> byBaseEntityByTypeStatus = new HashMap<>();
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typeDesignations.forEach(td -> mapTypeDesignation(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(Map<TypedEntityReference, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> 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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Map<TypeDesignationStatusBase<?>, Collection<EntityReference>> stringsOrderdByType;
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if(!byBaseEntityByTypeStatus.containsKey(baseEntityReference)){
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byBaseEntityByTypeStatus.put(baseEntityReference, new LinkedHashMap<>());
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}
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stringsOrderdByType = byBaseEntityByTypeStatus.get(baseEntityReference);
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// the cdm ordered term bases are ordered inverse, fixing this for here
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if(status == null){
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status = SpecimenTypeDesignationStatus.TYPE();
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}
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if(!stringsOrderdByType.containsKey(status)){
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stringsOrderdByType.put(status, new ArrayList<EntityReference>());
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}
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stringsOrderdByType.get(status).add(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, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> orderByTypeByBaseEntity(
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Map<TypedEntityReference, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> 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, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> stringsOrderedbyBaseEntityOrderdByType = new LinkedHashMap<>(stringsByTypeByBaseEntity.size());
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for(TypedEntityReference baseEntityRef : baseEntityKeyList){
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Map<TypeDesignationStatusBase<?>, Collection<EntityReference>> stringsByType = stringsByTypeByBaseEntity.get(baseEntityRef);
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// order the TypeDesignationStatusBase keys
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List<TypeDesignationStatusBase<?>> keyList = new LinkedList<>(stringsByType.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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LinkedHashMap<TypeDesignationStatusBase<?>, Collection<EntityReference>> orderedStringsByOrderedTypes = new LinkedHashMap<>();
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keyList.forEach(key -> orderedStringsByOrderedTypes.put(key, stringsByType.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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StringBuilder sb = new StringBuilder();
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if(getTypifiedNameCache() != null){
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sb.append(getTypifiedNameCache()).append(" ");
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}
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int typeCount = 0;
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for(TypedEntityReference baseEntityRef : orderedByTypesByBaseEntity.keySet()) {
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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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Map<TypeDesignationStatusBase<?>, Collection<EntityReference>> orderedRepresentations = 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 : orderedRepresentations.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 = orderedRepresentations.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 : orderedRepresentations.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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};
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finalString = sb.toString();
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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, Map<TypeDesignationStatusBase<?>, Collection<EntityReference>>> getOrderedTypeDesignations() {
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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()){
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sb.append(" rejected");
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}
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if(td.isConservedType()){
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sb.append(" conserved");
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}
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return sb.toString();
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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(SpecimenTypeDesignation td, boolean useFullTitleCache) {
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String result = "";
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if(useFullTitleCache){
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if(td.getTypeSpecimen() != null){
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String nameTitleCache = td.getTypeSpecimen().getTitleCache();
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if(getTypifiedNameCache() != null){
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nameTitleCache = nameTitleCache.replace(getTypifiedNameCache(), "");
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}
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result += nameTitleCache;
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}
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} else {
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if(td.getTypeSpecimen() != null){
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DerivedUnit du = td.getTypeSpecimen();
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if(du.isProtectedTitleCache()){
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result += du.getTitleCache();
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} else {
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DerivedUnitFacadeCacheStrategy cacheStrategy = new DerivedUnitFacadeCacheStrategy();
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result += cacheStrategy.getTitleCache(du, true);
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}
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}
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}
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if(td.getCitation() != null){
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result += " " + td.getCitation().getTitleCache();
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if(td.getCitationMicroReference() != null){
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result += " :" + td.getCitationMicroReference();
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}
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}
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if(td.isNotDesignated()){
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result += " not designated";
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}
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return result;
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}
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/**
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* @param td
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* @return
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* @deprecated
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*/
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@Deprecated
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private FieldUnit findFieldUnit(SpecimenTypeDesignation td) {
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DerivedUnit du = td.getTypeSpecimen();
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return findFieldUnit(du);
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}
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private FieldUnit findFieldUnit(DerivedUnit du) {
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if(du == null || du.getOriginals() == null){
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|
return null;
|
445
|
}
|
446
|
@SuppressWarnings("rawtypes")
|
447
|
Set<SpecimenOrObservationBase> originals = du.getDerivedFrom().getOriginals();
|
448
|
@SuppressWarnings("rawtypes")
|
449
|
Optional<SpecimenOrObservationBase> fieldUnit = originals.stream()
|
450
|
.filter(original -> original instanceof FieldUnit).findFirst();
|
451
|
if (fieldUnit.isPresent()) {
|
452
|
return (FieldUnit) fieldUnit.get();
|
453
|
} else {
|
454
|
for (@SuppressWarnings("rawtypes")
|
455
|
SpecimenOrObservationBase sob : originals) {
|
456
|
if (sob instanceof DerivedUnit) {
|
457
|
FieldUnit fu = findFieldUnit((DerivedUnit) sob);
|
458
|
if (fu != null) {
|
459
|
return fu;
|
460
|
}
|
461
|
}
|
462
|
}
|
463
|
}
|
464
|
|
465
|
return null;
|
466
|
}
|
467
|
|
468
|
|
469
|
public String print() {
|
470
|
return finalString;
|
471
|
}
|
472
|
|
473
|
/**
|
474
|
*
|
475
|
* @author a.kohlbecker
|
476
|
* @since Jun 12, 2017
|
477
|
*
|
478
|
*/
|
479
|
public class FieldUnitOrTypeName {
|
480
|
|
481
|
FieldUnit fieldUnit = null;
|
482
|
|
483
|
TaxonName typeName = null;
|
484
|
|
485
|
/**
|
486
|
* @param fieldUnit
|
487
|
* @param typeName
|
488
|
*/
|
489
|
private FieldUnitOrTypeName(FieldUnit fieldUnit, TaxonName typeName) {
|
490
|
this.fieldUnit = fieldUnit;
|
491
|
this.typeName = typeName;
|
492
|
if(fieldUnit != null && typeName != null){
|
493
|
throw new RuntimeException("FieldUnitOrTypeName must not contain two non null fields");
|
494
|
}
|
495
|
|
496
|
if(fieldUnit == null && typeName == null){
|
497
|
throw new NullPointerException("FieldUnitOrTypeName must not contain two null fields");
|
498
|
}
|
499
|
}
|
500
|
|
501
|
/**
|
502
|
* @return the fieldUnit
|
503
|
*/
|
504
|
public FieldUnit getFieldUnit() {
|
505
|
return fieldUnit;
|
506
|
}
|
507
|
|
508
|
/**
|
509
|
* @return the typeName
|
510
|
*/
|
511
|
public TaxonName getTypeName() {
|
512
|
return typeName;
|
513
|
}
|
514
|
|
515
|
/**
|
516
|
* @return the fieldUnit
|
517
|
*/
|
518
|
public boolean isFieldUnit() {
|
519
|
return fieldUnit != null;
|
520
|
}
|
521
|
|
522
|
/**
|
523
|
* @return the typeName
|
524
|
*/
|
525
|
public boolean isTypeName() {
|
526
|
return typeName != null;
|
527
|
}
|
528
|
|
529
|
public int getEntitiyId() {
|
530
|
if(isFieldUnit()){
|
531
|
return fieldUnit.getId();
|
532
|
} else {
|
533
|
return typeName.getId();
|
534
|
}
|
535
|
}
|
536
|
|
537
|
/**
|
538
|
* @return
|
539
|
*/
|
540
|
public String getTypeLabel() {
|
541
|
if(isFieldUnit()){
|
542
|
return "Type";
|
543
|
} else {
|
544
|
return "NameType";
|
545
|
}
|
546
|
}
|
547
|
|
548
|
/**
|
549
|
* @return
|
550
|
*/
|
551
|
public String getTitleCache() {
|
552
|
if(isFieldUnit()){
|
553
|
return fieldUnit.getTitleCache();
|
554
|
} else {
|
555
|
return typeName.getTitleCache();
|
556
|
}
|
557
|
}
|
558
|
|
559
|
public boolean matches(FieldUnit fieldUnit, TaxonName typeName){
|
560
|
boolean fuMatch = this.fieldUnit == null && fieldUnit == null || this.fieldUnit.equals(fieldUnit);
|
561
|
boolean nameMatch = this.typeName == null && typeName == null || this.typeName.equals(typeName);
|
562
|
return fuMatch && nameMatch;
|
563
|
}
|
564
|
|
565
|
|
566
|
|
567
|
|
568
|
}
|
569
|
}
|