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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.api.service.dto;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.joda.time.DateTime;
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import eu.etaxonomy.cdm.api.service.exception.RegistrationValidationException;
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import eu.etaxonomy.cdm.api.service.name.TypeDesignationDTO;
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import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetFormatter;
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import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager;
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import eu.etaxonomy.cdm.api.service.name.TypeDesignationWorkingSet;
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import eu.etaxonomy.cdm.format.reference.NomenclaturalSourceFormatter;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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import eu.etaxonomy.cdm.model.common.VersionableEntity;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.Registration;
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import eu.etaxonomy.cdm.model.name.RegistrationStatus;
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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.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.model.reference.NamedSourceBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.ref.EntityReference;
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import eu.etaxonomy.cdm.ref.TypedEntityReference;
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import eu.etaxonomy.cdm.strategy.cache.TagEnum;
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import eu.etaxonomy.cdm.strategy.cache.TaggedCacheHelper;
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import eu.etaxonomy.cdm.strategy.cache.TaggedText;
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public class RegistrationDTO {
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private static final Logger logger = LogManager.getLogger(RegistrationDTO.class);
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private String summary = "";
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private RegistrationType registrationType;
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private Reference citation = null;
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private String citationDetail = null;
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private String submitterUserName = null;
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private EntityReference name = null;
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private TypeDesignationSetManager typeDesignationManager;
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private Registration reg;
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private List<String> validationProblems = new ArrayList<>();
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private Set<TypedEntityReference<Registration>> blockedBy;
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private List<TaggedText> summaryTaggedText = new ArrayList<>();
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private String nomenclaturalCitationString;
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private String bibliographicCitationString;
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private String bibliographicInRefCitationString;
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/**
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* @param reg
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* @param typifiedName should be provided for registrations for TypeDesignations
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* @throws RegistrationValidationException
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*/
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public RegistrationDTO(Registration reg) {
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this.reg = reg;
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registrationType = RegistrationType.from(reg);
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if(reg.getSubmitter() != null ){
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submitterUserName = reg.getSubmitter().getUsername();
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}
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if(hasName(reg)){
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name = new EntityReference(reg.getName().getUuid(), reg.getName().getTitleCache());
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}
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NamedSourceBase publishedUnit = findPublishedUnit(reg);
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if(publishedUnit != null) {
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citation = publishedUnit.getCitation();
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citationDetail = publishedUnit.getCitationMicroReference();
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}
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switch (registrationType) {
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case EMPTY:
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summary = "BLANK REGISTRATION";
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summaryTaggedText.addAll(Arrays.asList(new TaggedText(TagEnum.label, summary)));
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break;
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case NAME:
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summary = reg.getName().getTitleCache();
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summaryTaggedText.addAll(reg.getName().getTaggedName());
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break;
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case NAME_AND_TYPIFICATION:
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case TYPIFICATION:
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default:
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try {
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typeDesignationManager = new TypeDesignationSetManager(reg.getTypeDesignations());
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summaryTaggedText.addAll(new TypeDesignationSetFormatter(false, true, true)
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.toTaggedText(typeDesignationManager));
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summary = TaggedCacheHelper.createString(summaryTaggedText);
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} catch (RegistrationValidationException e) {
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validationProblems.add("Validation errors: " + e.getMessage());
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}
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break;
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}
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makeBibliographicCitationStrings();
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makeNomenclaturalCitationString();
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}
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/**
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* To create an initially empty DTO for which only the <code>typifiedName</code> and the <code>publication</code> are defined.
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* All TypeDesignations added to the <code>Registration</code> need to refer to the same <code>typifiedName</code> and must be
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* published in the same <code>publication</code>.
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*
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* @param reg
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* @param typifiedName
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*/
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public RegistrationDTO(Registration reg, TaxonName typifiedName, Reference publication) {
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this.reg = reg;
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citation = publication;
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// create a TypeDesignationSetManager with only a reference to the typifiedName for validation
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typeDesignationManager = new TypeDesignationSetManager(typifiedName);
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makeBibliographicCitationStrings();
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makeNomenclaturalCitationString();
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}
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public static NamedSourceBase findPublishedUnit(Registration reg) {
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NamedSourceBase publishedUnit = null;
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if(hasName(reg)){
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publishedUnit = reg.getName().getNomenclaturalSource();
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} else if(hasTypifications(reg)){
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if(!reg.getTypeDesignations().isEmpty()){
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for(TypeDesignationBase<?> td : reg.getTypeDesignations()){
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if(td.getDesignationSource() != null) {
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publishedUnit = td.getDesignationSource();
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}
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}
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}
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}
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return publishedUnit;
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}
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private static boolean hasTypifications(Registration reg) {
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return reg.getTypeDesignations() != null && reg.getTypeDesignations().size() > 0;
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}
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private static boolean hasName(Registration reg) {
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return reg.getName() != null;
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}
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/**
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* Provides access to the Registration entity this DTO has been build from.
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* This method is purposely not a getter to hide the original Registration
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* from generic processes which are exposing, binding bean properties.
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*IReference
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* @return
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*/
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public Registration registration() {
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return reg;
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}
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public String getSummary() {
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return summary;
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}
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public List<TaggedText> getSummaryTaggedText() {
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return summaryTaggedText;
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}
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public String getSubmitterUserName(){
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return submitterUserName;
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}
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public RegistrationType getRegistrationType() {
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return registrationType;
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}
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public RegistrationStatus getStatus() {
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return reg.getStatus();
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}
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public String getIdentifier() {
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return reg.getIdentifier();
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}
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public UUID getUuid() {
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return reg.getUuid();
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}
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public String getSpecificIdentifier() {
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return reg.getSpecificIdentifier();
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}
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public DateTime getRegistrationDate() {
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return reg.getRegistrationDate();
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}
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public String getInstitutionTitleCache(){
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return reg.getInstitution() != null ? reg.getInstitution().getName() : null;
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}
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public VerbatimTimePeriod getDatePublished() {
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return citation == null ? null : citation.getDatePublished();
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}
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public DateTime getCreated() {
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return reg.getCreated();
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}
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public Reference getCitation() {
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return citation;
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}
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public void setCitation(Reference citation) throws Exception {
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if(this.citation == null){
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this.citation = citation;
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} else {
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throw new Exception("Can not set the citation on a non emtpy RegistrationDTO");
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}
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makeBibliographicCitationStrings();
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makeNomenclaturalCitationString();
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}
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public UUID getCitationUuid() {
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return citation == null ? null : citation.getUuid();
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}
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public EntityReference getTypifiedNameRef() {
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return typeDesignationManager != null ? typeDesignationManager.getTypifiedNameAsEntityRef() : null;
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}
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public TaxonName typifiedName() {
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return typeDesignationManager != null ? typeDesignationManager.getTypifiedName() : null;
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}
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public EntityReference getNameRef() {
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return name;
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}
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public Map<TypedEntityReference<? extends VersionableEntity>, TypeDesignationWorkingSet> getOrderedTypeDesignationWorkingSets() {
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return typeDesignationManager != null ? typeDesignationManager.getOrderedTypeDesignationWorkingSets() : null;
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}
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public TypeDesignationWorkingSet getTypeDesignationWorkingSet(TypedEntityReference baseEntityReference) {
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return typeDesignationManager != null ? typeDesignationManager.getOrderedTypeDesignationWorkingSets().get(baseEntityReference) : null;
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}
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public Set<TypeDesignationBase> getTypeDesignationsInWorkingSet(TypedEntityReference baseEntityReference) {
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Set<TypeDesignationBase> typeDesignations = new HashSet<>();
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TypeDesignationWorkingSet workingSet = getTypeDesignationWorkingSet(baseEntityReference);
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for(TypeDesignationDTO<?> ref : workingSet.getTypeDesignations()){
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typeDesignations.add(findTypeDesignation(ref));
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}
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return typeDesignations;
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}
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public NameTypeDesignation getNameTypeDesignation(TypedEntityReference baseEntityReference) {
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Set<TypeDesignationBase> typeDesignations = getTypeDesignationsInWorkingSet(baseEntityReference);
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if(typeDesignations.size() == 1){
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TypeDesignationBase<?> item = typeDesignations.iterator().next();
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return (NameTypeDesignation)item ;
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}
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if(typeDesignations.size() == 0){
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return null;
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}
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if(typeDesignations.size() > 1){
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throw new RuntimeException("Workingsets of NameTypeDesignations must contain exactly one item.");
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}
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return null;
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}
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private TypeDesignationBase<?> findTypeDesignation(TypeDesignationDTO ref) {
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return typeDesignationManager != null ? typeDesignationManager.findTypeDesignation(ref.getUuid()) : null;
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}
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public Collection<TypeDesignationBase<?>> typeDesignations() {
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return typeDesignationManager != null ? typeDesignationManager.getTypeDesignations() : null;
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}
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private void makeNomenclaturalCitationString() {
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if(citation == null){
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nomenclaturalCitationString = null;
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} else {
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if(INomenclaturalReference.class.isAssignableFrom(citation.getClass())){
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nomenclaturalCitationString = NomenclaturalSourceFormatter.INSTANCE().format(citation, citationDetail);
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} else {
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logger.error("The citation is not a NomenclaturalReference");
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nomenclaturalCitationString = citation.generateTitle();
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}
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}
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}
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private void makeBibliographicCitationStrings() {
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if(citation == null){
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bibliographicCitationString = null;
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} else {
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Reference bibliographicCitation;
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String bibliographicCitationDetail = citationDetail;
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if((citation.getType() == ReferenceType.Section || citation.getType() == ReferenceType.BookSection) && citation.getInReference() != null){
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bibliographicCitation = citation.getInReference();
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bibliographicCitationDetail = null; // can possibly be known once https://dev.e-taxonomy.eu/redmine/issues/6623 is solved
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} else {
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bibliographicCitation = citation;
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}
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if(StringUtils.isNotEmpty(bibliographicCitationDetail)){
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// TODO see https://dev.e-taxonomy.eu/redmine/issues/6623
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bibliographicInRefCitationString = bibliographicCitation.generateTitle().replaceAll("\\.$", "") + (StringUtils.isNotEmpty(bibliographicCitationDetail) ? ": " + bibliographicCitationDetail : "");
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} else {
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bibliographicInRefCitationString = bibliographicCitation.generateTitle();
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}
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if(StringUtils.isNotEmpty(citationDetail)){
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// TODO see https://dev.e-taxonomy.eu/redmine/issues/6623
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bibliographicCitationString = citation.generateTitle().replaceAll("\\.$", "") + (StringUtils.isNotEmpty(citationDetail) ? ": " + citationDetail : "");
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} else {
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bibliographicCitationString = citation.generateTitle();
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}
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}
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}
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/**
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* The nomenclatural citation is always the nomenclaturalCitation of the reference which is directly
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* associated with the registration.
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* <p>
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* <b>Note:</b>Compare with {@link #getBibliographicCitationString()}
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*
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* @return the nomenclaturalCitationString
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*/
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public String getNomenclaturalCitationString() {
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return nomenclaturalCitationString;
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}
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/**
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* The bibliographic in-reference citation is either taken from the reference which is directly
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* associated with the registration. In case this reference is a {@link eu.etaxonomy.cdm.model.reference.ReferenceType#Section} or
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* {@link eu.etaxonomy.cdm.model.reference.ReferenceType#BookSection} the inReference will be taken instead.
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* <p>
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* <b>Note:</b>Compare with {@link #getBibliographicCitationString()}
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*
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* @return the bibliographicInRefCitationString
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*/
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public String getBibliographicInRefCitationString() {
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return bibliographicInRefCitationString;
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}
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/**
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* The bibliographic citation is either reference which is directly
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* associated with the registration.
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* <p>
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* <b>Note:</b>Compare with {@link #getBibliographicInRefCitationString()}
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*
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* @return the bibliographicCitationString
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*/
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public String getBibliographicCitationString() {
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return bibliographicCitationString;
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}
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|
public boolean isBlocked() {
|
|
379
|
return reg.getBlockedBy() != null && !reg.getBlockedBy().isEmpty();
|
|
380
|
}
|
|
381
|
|
|
382
|
/**
|
|
383
|
* @return the blockedBy
|
|
384
|
*/
|
|
385
|
public Set<TypedEntityReference<Registration>> getBlockedBy() {
|
|
386
|
|
|
387
|
if(blockedBy == null){
|
|
388
|
blockedBy = new HashSet<>();
|
|
389
|
if(reg.getBlockedBy() != null){
|
|
390
|
for(Registration blockReg : reg.getBlockedBy()){
|
|
391
|
blockedBy.add(new TypedEntityReference<Registration>(Registration.class, blockReg.getUuid(), blockReg.getIdentifier()));
|
|
392
|
}
|
|
393
|
}
|
|
394
|
}
|
|
395
|
return blockedBy;
|
|
396
|
}
|
|
397
|
|
|
398
|
public List<String> getValidationProblems() {
|
|
399
|
return validationProblems;
|
|
400
|
}
|
|
401
|
|
|
402
|
public boolean isPersisted() {
|
|
403
|
return reg.isPersited();
|
|
404
|
}
|
|
405
|
}
|