Revision 76f89a6f
Added by Andreas Kohlbecker over 12 years ago
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java | ||
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// $Id$ |
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy
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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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* |
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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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@Service |
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@Transactional(propagation = Propagation.SUPPORTS, readOnly = true) |
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public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService{
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private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);
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@Autowired
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private ITaxonNameDao nameDao;
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@Autowired
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private IOrderedTermVocabularyDao orderedVocabularyDao;
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/**
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* Constructor
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*/
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public TaxonServiceImpl(){
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if (logger.isDebugEnabled()) { logger.debug("Load TaxonService Bean"); }
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}
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/**
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* FIXME Candidate for harmonization
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* rename searchByName ?
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*/
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public List<TaxonBase> searchTaxaByName(String name, Reference sec) {
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return dao.getTaxaByName(name, sec);
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}
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/**
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* FIXME Candidate for harmonization
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* list(Synonym.class, ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllSynonyms(int, int)
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*/
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public List<Synonym> getAllSynonyms(int limit, int start) {
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return dao.getAllSynonyms(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* list(Taxon.class, ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllTaxa(int, int)
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*/
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public List<Taxon> getAllTaxa(int limit, int start) {
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return dao.getAllTaxa(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* merge with getRootTaxa(Reference sec, ..., ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean)
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*/
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public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
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if (cdmFetch == null){
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cdmFetch = CdmFetch.NO_FETCH();
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}
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return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,boolean withMisapplications, List<String> propertyPaths) {
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return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllRelationships(int, int)
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*/
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public List<RelationshipBase> getAllRelationships(int limit, int start){
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return dao.getAllRelationships(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ?
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*/
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@Deprecated
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public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
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String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
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UUID uuid = UUID.fromString(taxonRelTypeVocabularyId);
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OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary =
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(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
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return taxonRelTypeVocabulary;
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)
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*/
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@Transactional(readOnly = false)
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public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){
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TaxonNameBase synonymName = synonym.getName();
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synonymName.removeTaxonBase(synonym);
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TaxonNameBase taxonName = acceptedTaxon.getName();
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taxonName.removeTaxonBase(acceptedTaxon);
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synonym.setName(taxonName);
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acceptedTaxon.setName(synonymName);
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// the accepted taxon needs a new uuid because the concept has changed
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// FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"
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//acceptedTaxon.setUuid(UUID.randomUUID());
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
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*/
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//TODO correct delete handling still needs to be implemented / checked
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@Override
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@Transactional(readOnly = false)
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public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws IllegalArgumentException{
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TaxonNameBase acceptedName = acceptedTaxon.getName();
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TaxonNameBase synonymName = synonym.getName();
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HomotypicalGroup synonymHomotypicGroup = synonymName.getHomotypicalGroup();
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if (acceptedName.getHomotypicalGroup().equals(synonymHomotypicGroup)){
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String message = "The accepted taxon and the synonym are part of the same homotypical group and therefore can not be both accepted.";
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throw new IllegalArgumentException(message);
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}
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Taxon newAcceptedTaxon = Taxon.NewInstance(synonymName, acceptedTaxon.getSec());
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SynonymRelationshipType relType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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List<Synonym> heteroSynonyms = synonymHomotypicGroup.getSynonymsInGroup(acceptedTaxon.getSec());
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for (Synonym heteroSynonym : heteroSynonyms){
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if (synonym.equals(heteroSynonym)){
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acceptedTaxon.removeSynonym(heteroSynonym, false);
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}else{
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heteroSynonym.replaceAcceptedTaxon(newAcceptedTaxon, relType, copyCitationInfo, citation, microCitation);
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}
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}
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//synonym.getName().removeTaxonBase(synonym);
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//TODO correct delete handling still needs to be implemented / checked
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if (deleteSynonym){
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try {
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this.dao.flush();
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this.delete(synonym);
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} catch (Exception e) {
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logger.info("Can't delete old synonym from database");
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}
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}
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return newAcceptedTaxon;
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}
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public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){
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// Get name from synonym
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TaxonNameBase<?, ?> synonymName = synonym.getName();
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// remove synonym from taxon
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toTaxon.removeSynonym(synonym);
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// Create a taxon with synonym name
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Taxon fromTaxon = Taxon.NewInstance(synonymName, null);
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// Add taxon relation
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fromTaxon.addTaxonRelation(toTaxon, taxonRelationshipType, citation, microcitation);
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// since we are swapping names, we have to detach the name from the synonym completely.
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// Otherwise the synonym will still be in the list of typified names.
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synonym.getName().removeTaxonBase(synonym);
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return fromTaxon;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeHomotypicalGroupOfSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)
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*/
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@Transactional(readOnly = false)
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@Override
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public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
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boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable){
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// Get synonym name
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TaxonNameBase synonymName = synonym.getName();
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HomotypicalGroup oldHomotypicalGroup = synonymName.getHomotypicalGroup();
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// Switch groups
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oldHomotypicalGroup.removeTypifiedName(synonymName);
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newHomotypicalGroup.addTypifiedName(synonymName);
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//remove existing basionym relationships
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synonymName.removeBasionyms();
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//add basionym relationship
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if (setBasionymRelationIfApplicable){
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Set<TaxonNameBase> basionyms = newHomotypicalGroup.getBasionyms();
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for (TaxonNameBase basionym : basionyms){
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synonymName.addBasionym(basionym);
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}
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}
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//set synonym relationship correctly
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private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);
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@Autowired
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private ITaxonNameDao nameDao;
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@Autowired
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private IOrderedTermVocabularyDao orderedVocabularyDao;
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/**
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* Constructor
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*/
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public TaxonServiceImpl(){
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if (logger.isDebugEnabled()) { logger.debug("Load TaxonService Bean"); }
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}
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/**
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* FIXME Candidate for harmonization
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* rename searchByName ?
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*/
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public List<TaxonBase> searchTaxaByName(String name, Reference sec) {
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return dao.getTaxaByName(name, sec);
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}
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/**
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* FIXME Candidate for harmonization
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* list(Synonym.class, ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllSynonyms(int, int)
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*/
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public List<Synonym> getAllSynonyms(int limit, int start) {
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return dao.getAllSynonyms(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* list(Taxon.class, ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllTaxa(int, int)
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*/
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public List<Taxon> getAllTaxa(int limit, int start) {
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return dao.getAllTaxa(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* merge with getRootTaxa(Reference sec, ..., ...)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean)
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*/
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public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
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if (cdmFetch == null){
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cdmFetch = CdmFetch.NO_FETCH();
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}
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return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,boolean withMisapplications, List<String> propertyPaths) {
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return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllRelationships(int, int)
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*/
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public List<RelationshipBase> getAllRelationships(int limit, int start){
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return dao.getAllRelationships(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ?
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*/
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@Deprecated
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public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
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String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
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UUID uuid = UUID.fromString(taxonRelTypeVocabularyId);
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OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary =
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(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
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return taxonRelTypeVocabulary;
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}
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/*
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)
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*/
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@Transactional(readOnly = false)
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public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){
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TaxonNameBase synonymName = synonym.getName();
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synonymName.removeTaxonBase(synonym);
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TaxonNameBase taxonName = acceptedTaxon.getName();
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taxonName.removeTaxonBase(acceptedTaxon);
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synonym.setName(taxonName);
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acceptedTaxon.setName(synonymName);
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// the accepted taxon needs a new uuid because the concept has changed
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// FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"
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//acceptedTaxon.setUuid(UUID.randomUUID());
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
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*/
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//TODO correct delete handling still needs to be implemented / checked
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@Override
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@Transactional(readOnly = false)
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public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws IllegalArgumentException{
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TaxonNameBase acceptedName = acceptedTaxon.getName();
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TaxonNameBase synonymName = synonym.getName();
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HomotypicalGroup synonymHomotypicGroup = synonymName.getHomotypicalGroup();
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if (acceptedName.getHomotypicalGroup().equals(synonymHomotypicGroup)){
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String message = "The accepted taxon and the synonym are part of the same homotypical group and therefore can not be both accepted.";
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throw new IllegalArgumentException(message);
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}
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Taxon newAcceptedTaxon = Taxon.NewInstance(synonymName, acceptedTaxon.getSec());
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SynonymRelationshipType relType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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List<Synonym> heteroSynonyms = synonymHomotypicGroup.getSynonymsInGroup(acceptedTaxon.getSec());
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for (Synonym heteroSynonym : heteroSynonyms){
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if (synonym.equals(heteroSynonym)){
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acceptedTaxon.removeSynonym(heteroSynonym, false);
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}else{
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heteroSynonym.replaceAcceptedTaxon(newAcceptedTaxon, relType, copyCitationInfo, citation, microCitation);
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}
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}
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//synonym.getName().removeTaxonBase(synonym);
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//TODO correct delete handling still needs to be implemented / checked
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if (deleteSynonym){
|
|
| 210 |
try {
|
|
| 211 |
this.dao.flush();
|
|
| 212 |
this.delete(synonym);
|
|
| 213 |
|
|
| 214 |
} catch (Exception e) {
|
|
| 215 |
logger.info("Can't delete old synonym from database");
|
|
| 216 |
}
|
|
| 217 |
}
|
|
| 218 |
|
|
| 219 |
|
|
| 220 |
return newAcceptedTaxon;
|
|
| 221 |
}
|
|
| 222 |
|
|
| 223 |
public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){
|
|
| 224 |
|
|
| 225 |
// Get name from synonym
|
|
| 226 |
TaxonNameBase<?, ?> synonymName = synonym.getName();
|
|
| 227 |
|
|
| 228 |
// remove synonym from taxon
|
|
| 229 |
toTaxon.removeSynonym(synonym);
|
|
| 230 |
|
|
| 231 |
// Create a taxon with synonym name
|
|
| 232 |
Taxon fromTaxon = Taxon.NewInstance(synonymName, null);
|
|
| 233 |
|
|
| 234 |
// Add taxon relation
|
|
| 235 |
fromTaxon.addTaxonRelation(toTaxon, taxonRelationshipType, citation, microcitation);
|
|
| 236 |
|
|
| 237 |
// since we are swapping names, we have to detach the name from the synonym completely.
|
|
| 238 |
// Otherwise the synonym will still be in the list of typified names.
|
|
| 239 |
synonym.getName().removeTaxonBase(synonym);
|
|
| 240 |
|
|
| 241 |
return fromTaxon;
|
|
| 242 |
}
|
|
| 243 |
|
|
| 244 |
/* (non-Javadoc)
|
|
| 245 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeHomotypicalGroupOfSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)
|
|
| 246 |
*/
|
|
| 247 |
@Transactional(readOnly = false)
|
|
| 248 |
@Override
|
|
| 249 |
public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
|
|
| 250 |
boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable){
|
|
| 251 |
// Get synonym name
|
|
| 252 |
TaxonNameBase synonymName = synonym.getName();
|
|
| 253 |
HomotypicalGroup oldHomotypicalGroup = synonymName.getHomotypicalGroup();
|
|
| 254 |
|
|
| 255 |
|
|
| 256 |
// Switch groups
|
|
| 257 |
oldHomotypicalGroup.removeTypifiedName(synonymName);
|
|
| 258 |
newHomotypicalGroup.addTypifiedName(synonymName);
|
|
| 259 |
|
|
| 260 |
//remove existing basionym relationships
|
|
| 261 |
synonymName.removeBasionyms();
|
|
| 262 |
|
|
| 263 |
//add basionym relationship
|
|
| 264 |
if (setBasionymRelationIfApplicable){
|
|
| 265 |
Set<TaxonNameBase> basionyms = newHomotypicalGroup.getBasionyms();
|
|
| 266 |
for (TaxonNameBase basionym : basionyms){
|
|
| 267 |
synonymName.addBasionym(basionym);
|
|
| 268 |
}
|
|
| 269 |
}
|
|
| 270 |
|
|
| 271 |
//set synonym relationship correctly
|
|
| 272 | 272 |
// SynonymRelationship relToTaxon = null; |
| 273 |
boolean relToTargetTaxonExists = false;
|
|
| 274 |
Set<SynonymRelationship> existingRelations = synonym.getSynonymRelations();
|
|
| 275 |
for (SynonymRelationship rel : existingRelations){
|
|
| 276 |
Taxon acceptedTaxon = rel.getAcceptedTaxon();
|
|
| 277 |
boolean isTargetTaxon = acceptedTaxon != null && acceptedTaxon.equals(targetTaxon);
|
|
| 278 |
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
|
| 279 |
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
|
| 280 |
SynonymRelationshipType newRelationType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
|
| 281 |
rel.setType(newRelationType);
|
|
| 282 |
//TODO handle citation and microCitation
|
|
| 283 |
|
|
| 284 |
if (isTargetTaxon){
|
|
| 285 |
relToTargetTaxonExists = true;
|
|
| 286 |
}else{
|
|
| 287 |
if (removeFromOtherTaxa){
|
|
| 288 |
acceptedTaxon.removeSynonym(synonym, false);
|
|
| 289 |
}else{
|
|
| 290 |
//do nothing
|
|
| 291 |
}
|
|
| 292 |
}
|
|
| 293 |
}
|
|
| 294 |
if (targetTaxon != null && ! relToTargetTaxonExists ){
|
|
| 295 |
Taxon acceptedTaxon = targetTaxon;
|
|
| 296 |
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
|
| 297 |
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
|
| 298 |
SynonymRelationshipType relType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
|
| 299 |
//TODO handle citation and microCitation
|
|
| 300 |
Reference citation = null;
|
|
| 301 |
String microCitation = null;
|
|
| 302 |
acceptedTaxon.addSynonym(synonym, relType, citation, microCitation);
|
|
| 303 |
}
|
|
| 304 |
|
|
| 305 |
}
|
|
| 306 |
|
|
| 307 |
|
|
| 308 |
/* (non-Javadoc)
|
|
| 309 |
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
|
|
| 310 |
*/
|
|
| 311 |
@Override
|
|
| 312 |
public void updateTitleCache(Class<? extends TaxonBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy, IProgressMonitor monitor) {
|
|
| 313 |
if (clazz == null){
|
|
| 314 |
clazz = TaxonBase.class;
|
|
| 315 |
}
|
|
| 316 |
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
|
| 317 |
}
|
|
| 318 |
|
|
| 319 |
@Autowired
|
|
| 320 |
protected void setDao(ITaxonDao dao) {
|
|
| 321 |
this.dao = dao;
|
|
| 322 |
}
|
|
| 323 |
|
|
| 324 |
/* (non-Javadoc)
|
|
| 325 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
|
| 326 |
*/
|
|
| 327 |
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 273 |
boolean relToTargetTaxonExists = false;
|
|
| 274 |
Set<SynonymRelationship> existingRelations = synonym.getSynonymRelations();
|
|
| 275 |
for (SynonymRelationship rel : existingRelations){
|
|
| 276 |
Taxon acceptedTaxon = rel.getAcceptedTaxon();
|
|
| 277 |
boolean isTargetTaxon = acceptedTaxon != null && acceptedTaxon.equals(targetTaxon);
|
|
| 278 |
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
|
| 279 |
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
|
| 280 |
SynonymRelationshipType newRelationType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
|
| 281 |
rel.setType(newRelationType);
|
|
| 282 |
//TODO handle citation and microCitation
|
|
| 283 |
|
|
| 284 |
if (isTargetTaxon){
|
|
| 285 |
relToTargetTaxonExists = true;
|
|
| 286 |
}else{
|
|
| 287 |
if (removeFromOtherTaxa){
|
|
| 288 |
acceptedTaxon.removeSynonym(synonym, false);
|
|
| 289 |
}else{
|
|
| 290 |
//do nothing
|
|
| 291 |
}
|
|
| 292 |
}
|
|
| 293 |
}
|
|
| 294 |
if (targetTaxon != null && ! relToTargetTaxonExists ){
|
|
| 295 |
Taxon acceptedTaxon = targetTaxon;
|
|
| 296 |
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
|
| 297 |
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
|
| 298 |
SynonymRelationshipType relType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
|
| 299 |
//TODO handle citation and microCitation
|
|
| 300 |
Reference citation = null;
|
|
| 301 |
String microCitation = null;
|
|
| 302 |
acceptedTaxon.addSynonym(synonym, relType, citation, microCitation);
|
|
| 303 |
}
|
|
| 304 |
|
|
| 305 |
}
|
|
| 306 |
|
|
| 307 |
|
|
| 308 |
/* (non-Javadoc)
|
|
| 309 |
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
|
|
| 310 |
*/
|
|
| 311 |
@Override
|
|
| 312 |
public void updateTitleCache(Class<? extends TaxonBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy, IProgressMonitor monitor) {
|
|
| 313 |
if (clazz == null){
|
|
| 314 |
clazz = TaxonBase.class;
|
|
| 315 |
}
|
|
| 316 |
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
|
| 317 |
}
|
|
| 318 |
|
|
| 319 |
@Autowired
|
|
| 320 |
protected void setDao(ITaxonDao dao) {
|
|
| 321 |
this.dao = dao;
|
|
| 322 |
}
|
|
| 323 |
|
|
| 324 |
/* (non-Javadoc)
|
|
| 325 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
|
| 326 |
*/
|
|
| 327 |
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 328 | 328 |
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank); |
| 329 |
|
|
| 330 |
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
| 331 |
if(numberOfResults > 0) { // no point checking again
|
|
| 332 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
|
| 333 |
}
|
|
| 334 |
|
|
| 335 |
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
|
|
| 336 |
}
|
|
| 337 |
|
|
| 338 |
/* (non-Javadoc)
|
|
| 339 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
|
| 340 |
*/
|
|
| 341 |
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 329 |
|
|
| 330 |
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
| 331 |
if(numberOfResults > 0) { // no point checking again
|
|
| 332 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
|
| 333 |
}
|
|
| 334 |
|
|
| 335 |
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
|
|
| 336 |
}
|
|
| 337 |
|
|
| 338 |
/* (non-Javadoc)
|
|
| 339 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
|
| 340 |
*/
|
|
| 341 |
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 342 | 342 |
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank); |
| 343 |
|
|
| 344 |
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
| 345 |
if(numberOfResults > 0) { // no point checking again
|
|
| 346 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
|
| 347 |
}
|
|
| 348 |
|
|
| 349 |
return results;
|
|
| 350 |
}
|
|
| 351 |
|
|
| 352 |
/* (non-Javadoc)
|
|
| 353 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
| 354 |
*/
|
|
| 355 |
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
|
| 356 |
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
|
| 357 |
|
|
| 358 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
| 359 |
if(numberOfResults > 0) { // no point checking again
|
|
| 360 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
| 361 |
}
|
|
| 362 |
return results;
|
|
| 363 |
}
|
|
| 364 |
|
|
| 365 |
/* (non-Javadoc)
|
|
| 366 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
| 367 |
*/
|
|
| 368 |
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 343 |
|
|
| 344 |
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
|
| 345 |
if(numberOfResults > 0) { // no point checking again
|
|
| 346 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
|
| 347 |
}
|
|
| 348 |
|
|
| 349 |
return results;
|
|
| 350 |
}
|
|
| 351 |
|
|
| 352 |
/* (non-Javadoc)
|
|
| 353 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
| 354 |
*/
|
|
| 355 |
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
|
| 356 |
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
|
| 357 |
|
|
| 358 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
|
| 359 |
if(numberOfResults > 0) { // no point checking again
|
|
| 360 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
| 361 |
}
|
|
| 362 |
return results;
|
|
| 363 |
}
|
|
| 364 |
|
|
| 365 |
/* (non-Javadoc)
|
|
| 366 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
| 367 |
*/
|
|
| 368 |
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 369 | 369 |
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo); |
| 370 |
|
|
| 371 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>(); |
|
| 372 |
if(numberOfResults > 0) { // no point checking again
|
|
| 373 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo); |
|
| 374 |
} |
|
| 375 |
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results); |
|
| 376 |
} |
|
| 377 |
|
|
| 378 |
/* (non-Javadoc) |
|
| 379 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List) |
|
| 380 |
*/ |
|
| 381 |
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
|
| 382 |
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom); |
|
| 383 |
|
|
| 384 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>(); |
|
| 385 |
if(numberOfResults > 0) { // no point checking again
|
|
| 386 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom); |
|
| 387 |
} |
|
| 388 |
return results; |
|
| 389 |
} |
|
| 390 |
|
|
| 391 |
/* (non-Javadoc) |
|
| 392 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List) |
|
| 393 |
*/ |
|
| 394 |
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 370 |
|
|
| 371 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>(); |
|
| 372 |
if(numberOfResults > 0) { // no point checking again
|
|
| 373 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo); |
|
| 374 |
} |
|
| 375 |
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results); |
|
| 376 |
} |
|
| 377 |
|
|
| 378 |
/* (non-Javadoc) |
|
| 379 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List) |
|
| 380 |
*/ |
|
| 381 |
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
|
| 395 | 382 |
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom); |
| 396 |
|
|
| 397 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>(); |
|
| 398 |
if(numberOfResults > 0) { // no point checking again
|
|
| 399 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom); |
|
| 400 |
} |
|
| 401 |
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results); |
|
| 402 |
} |
|
| 403 |
|
|
| 404 |
/* (non-Javadoc) |
|
| 405 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List) |
|
| 406 |
*/ |
|
| 407 |
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 383 |
|
|
| 384 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>(); |
|
| 385 |
if(numberOfResults > 0) { // no point checking again
|
|
| 386 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom); |
|
| 387 |
} |
|
| 388 |
return results; |
|
| 389 |
} |
|
| 390 |
|
|
| 391 |
/* (non-Javadoc) |
|
| 392 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List) |
|
| 393 |
*/ |
|
| 394 |
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 395 |
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom); |
|
| 396 |
|
|
| 397 |
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>(); |
|
| 398 |
if(numberOfResults > 0) { // no point checking again
|
|
| 399 |
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom); |
|
| 400 |
} |
|
| 401 |
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results); |
|
| 402 |
} |
|
| 403 |
|
|
| 404 |
/* (non-Javadoc) |
|
| 405 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List) |
|
| 406 |
*/ |
|
| 407 |
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 408 | 408 |
Integer numberOfResults = dao.countSynonyms(taxon, type); |
| 409 |
|
|
| 410 |
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
| 411 |
if(numberOfResults > 0) { // no point checking again
|
|
| 412 |
results = dao.getSynonyms(taxon, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
| 413 |
}
|
|
| 414 |
|
|
| 415 |
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
| 416 |
}
|
|
| 417 |
|
|
| 418 |
/* (non-Javadoc)
|
|
| 419 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
| 420 |
*/
|
|
| 421 |
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 409 |
|
|
| 410 |
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
| 411 |
if(numberOfResults > 0) { // no point checking again
|
|
| 412 |
results = dao.getSynonyms(taxon, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
| 413 |
}
|
|
| 414 |
|
|
| 415 |
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
| 416 |
}
|
|
| 417 |
|
|
| 418 |
/* (non-Javadoc)
|
|
| 419 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
|
| 420 |
*/
|
|
| 421 |
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
| 422 | 422 |
Integer numberOfResults = dao.countSynonyms(synonym, type); |
| 423 |
|
|
| 424 |
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
| 425 |
if(numberOfResults > 0) { // no point checking again
|
|
| 426 |
results = dao.getSynonyms(synonym, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
| 427 |
}
|
|
| 428 |
|
|
| 429 |
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
| 430 |
}
|
|
| 431 |
|
|
| 432 |
/* (non-Javadoc)
|
|
| 433 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHomotypicSynonymsByHomotypicGroup(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
|
| 434 |
*/
|
|
| 435 |
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
|
|
| 436 |
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
| 437 |
return t.getHomotypicSynonymsByHomotypicGroup();
|
|
| 438 |
}
|
|
| 439 |
|
|
| 440 |
/* (non-Javadoc)
|
|
| 441 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHeterotypicSynonymyGroups(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
|
| 442 |
*/
|
|
| 443 |
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
|
|
| 444 |
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
| 445 |
List<HomotypicalGroup> hsgl = t.getHeterotypicSynonymyGroups();
|
|
| 446 |
List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(hsgl.size());
|
|
| 447 |
for(HomotypicalGroup hsg : hsgl){
|
|
| 448 |
heterotypicSynonymyGroups.add(hsg.getSynonymsInGroup(t.getSec()));
|
|
| 449 |
}
|
|
| 450 |
return heterotypicSynonymyGroups;
|
|
| 451 |
}
|
|
| 452 |
|
|
| 453 |
public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(ITaxonServiceConfigurator configurator){
|
|
| 454 |
|
|
| 455 |
List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();
|
|
| 456 |
Class<? extends TaxonBase> clazz = null;
|
|
| 457 |
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
|
| 458 |
clazz = TaxonBase.class;
|
|
| 459 |
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
| 460 |
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
|
| 461 |
} else if(configurator.isDoTaxa()) {
|
|
| 462 |
clazz = Taxon.class;
|
|
| 463 |
//propertyPath = configurator.getTaxonPropertyPath();
|
|
| 464 |
} else if (configurator.isDoSynonyms()) {
|
|
| 465 |
clazz = Synonym.class;
|
|
| 466 |
//propertyPath = configurator.getSynonymPropertyPath();
|
|
| 467 |
}
|
|
| 468 |
|
|
| 469 |
|
|
| 470 |
result = dao.getTaxaByNameForEditor(clazz, configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
|
| 471 |
return result;
|
|
| 472 |
}
|
|
| 473 |
/* (non-Javadoc)
|
|
| 474 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)
|
|
| 475 |
*/
|
|
| 476 |
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
|
| 477 |
|
|
| 478 |
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
|
| 479 |
int numberOfResults = 0; // overall number of results (as opposed to number of results per page)
|
|
| 480 |
List<TaxonBase> taxa = null;
|
|
| 481 |
|
|
| 482 |
// Taxa and synonyms
|
|
| 483 |
long numberTaxaResults = 0L;
|
|
| 484 |
|
|
| 485 |
Class<? extends TaxonBase> clazz = null;
|
|
| 486 |
List<String> propertyPath = new ArrayList<String>();
|
|
| 487 |
if(configurator.getTaxonPropertyPath() != null){
|
|
| 488 |
propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
| 489 |
}
|
|
| 490 |
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
|
| 491 |
clazz = TaxonBase.class;
|
|
| 492 |
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
| 493 |
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
|
| 494 |
} else if(configurator.isDoTaxa()) {
|
|
| 495 |
clazz = Taxon.class;
|
|
| 496 |
//propertyPath = configurator.getTaxonPropertyPath();
|
|
| 497 |
} else if (configurator.isDoSynonyms()) {
|
|
| 498 |
clazz = Synonym.class;
|
|
| 499 |
//propertyPath = configurator.getSynonymPropertyPath();
|
|
| 500 |
}
|
|
| 501 |
|
|
| 502 |
if(clazz != null){
|
|
| 503 |
if(configurator.getPageSize() != null){ // no point counting if we need all anyway
|
|
| 504 |
numberTaxaResults =
|
|
| 505 |
dao.countTaxaByName(clazz,
|
|
| 506 |
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
|
| 507 |
configurator.getNamedAreas());
|
|
| 508 |
}
|
|
| 509 |
|
|
| 510 |
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results
|
|
| 511 |
taxa = dao.getTaxaByName(clazz,
|
|
| 512 |
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
|
| 513 |
configurator.getNamedAreas(), configurator.getPageSize(),
|
|
| 514 |
configurator.getPageNumber(), propertyPath);
|
|
| 515 |
}
|
|
| 516 |
}
|
|
| 517 |
|
|
| 518 |
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
|
| 519 |
|
|
| 520 |
if(taxa != null){
|
|
| 521 |
results.addAll(taxa);
|
|
| 522 |
}
|
|
| 523 |
|
|
| 524 |
numberOfResults += numberTaxaResults;
|
|
| 525 |
|
|
| 526 |
// Names without taxa
|
|
| 527 |
if (configurator.isDoNamesWithoutTaxa()) {
|
|
| 423 |
|
|
| 424 |
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
|
| 425 |
if(numberOfResults > 0) { // no point checking again
|
|
| 426 |
results = dao.getSynonyms(synonym, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
| 427 |
}
|
|
| 428 |
|
|
| 429 |
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
| 430 |
}
|
|
| 431 |
|
|
| 432 |
/* (non-Javadoc)
|
|
| 433 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHomotypicSynonymsByHomotypicGroup(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
|
| 434 |
*/
|
|
| 435 |
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
|
|
| 436 |
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
| 437 |
return t.getHomotypicSynonymsByHomotypicGroup();
|
|
| 438 |
}
|
|
| 439 |
|
|
| 440 |
/* (non-Javadoc)
|
|
| 441 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHeterotypicSynonymyGroups(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
|
| 442 |
*/
|
|
| 443 |
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
|
|
| 444 |
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
|
| 445 |
List<HomotypicalGroup> hsgl = t.getHeterotypicSynonymyGroups();
|
|
| 446 |
List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(hsgl.size());
|
|
| 447 |
for(HomotypicalGroup hsg : hsgl){
|
|
| 448 |
heterotypicSynonymyGroups.add(hsg.getSynonymsInGroup(t.getSec()));
|
|
| 449 |
}
|
|
| 450 |
return heterotypicSynonymyGroups;
|
|
| 451 |
}
|
|
| 452 |
|
|
| 453 |
public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(ITaxonServiceConfigurator configurator){
|
|
| 454 |
|
|
| 455 |
List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();
|
|
| 456 |
Class<? extends TaxonBase> clazz = null;
|
|
| 457 |
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
|
| 458 |
clazz = TaxonBase.class;
|
|
| 459 |
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
| 460 |
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
|
| 461 |
} else if(configurator.isDoTaxa()) {
|
|
| 462 |
clazz = Taxon.class;
|
|
| 463 |
//propertyPath = configurator.getTaxonPropertyPath();
|
|
| 464 |
} else if (configurator.isDoSynonyms()) {
|
|
| 465 |
clazz = Synonym.class;
|
|
| 466 |
//propertyPath = configurator.getSynonymPropertyPath();
|
|
| 467 |
}
|
|
| 468 |
|
|
| 469 |
|
|
| 470 |
result = dao.getTaxaByNameForEditor(clazz, configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
|
| 471 |
return result;
|
|
| 472 |
}
|
|
| 473 |
/* (non-Javadoc)
|
|
| 474 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)
|
|
| 475 |
*/
|
|
| 476 |
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
|
| 477 |
|
|
| 478 |
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
|
| 479 |
int numberOfResults = 0; // overall number of results (as opposed to number of results per page)
|
|
| 480 |
List<TaxonBase> taxa = null;
|
|
| 481 |
|
|
| 482 |
// Taxa and synonyms
|
|
| 483 |
long numberTaxaResults = 0L;
|
|
| 484 |
|
|
| 485 |
Class<? extends TaxonBase> clazz = null;
|
|
| 486 |
List<String> propertyPath = new ArrayList<String>();
|
|
| 487 |
if(configurator.getTaxonPropertyPath() != null){
|
|
| 488 |
propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
| 489 |
}
|
|
| 490 |
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
|
| 491 |
clazz = TaxonBase.class;
|
|
| 492 |
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
|
| 493 |
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
|
| 494 |
} else if(configurator.isDoTaxa()) {
|
|
| 495 |
clazz = Taxon.class;
|
|
| 496 |
//propertyPath = configurator.getTaxonPropertyPath();
|
|
| 497 |
} else if (configurator.isDoSynonyms()) {
|
|
| 498 |
clazz = Synonym.class;
|
|
| 499 |
//propertyPath = configurator.getSynonymPropertyPath();
|
|
| 500 |
}
|
|
| 501 |
|
|
| 502 |
if(clazz != null){
|
|
| 503 |
if(configurator.getPageSize() != null){ // no point counting if we need all anyway
|
|
| 504 |
numberTaxaResults =
|
|
| 505 |
dao.countTaxaByName(clazz,
|
|
| 506 |
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
|
| 507 |
configurator.getNamedAreas());
|
|
| 508 |
}
|
|
| 509 |
|
|
| 510 |
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results
|
|
| 511 |
taxa = dao.getTaxaByName(clazz,
|
|
| 512 |
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
|
| 513 |
configurator.getNamedAreas(), configurator.getPageSize(),
|
|
| 514 |
configurator.getPageNumber(), propertyPath);
|
|
| 515 |
}
|
|
| 516 |
}
|
|
| 517 |
|
|
| 518 |
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
|
| 519 |
|
|
| 520 |
if(taxa != null){
|
|
| 521 |
results.addAll(taxa);
|
|
| 522 |
}
|
|
| 523 |
|
|
| 524 |
numberOfResults += numberTaxaResults;
|
|
| 525 |
|
|
| 526 |
// Names without taxa
|
|
| 527 |
if (configurator.isDoNamesWithoutTaxa()) {
|
|
| 528 | 528 |
int numberNameResults = 0; |
| 529 |
|
|
| 530 |
List<? extends TaxonNameBase<?,?>> names = |
|
| 531 |
nameDao.findByName(configurator.getTitleSearchStringSqlized(), configurator.getMatchMode(), |
|
| 532 |
configurator.getPageSize(), configurator.getPageNumber(), null, configurator.getTaxonNamePropertyPath()); |
|
| 533 |
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
|
| 534 |
if (names.size() > 0) {
|
|
| 535 |
for (TaxonNameBase<?,?> taxonName : names) {
|
|
| 536 |
if (taxonName.getTaxonBases().size() == 0) {
|
|
| 537 |
results.add(taxonName); |
|
| 538 |
numberNameResults++; |
|
| 539 |
} |
|
| 540 |
} |
|
| 541 |
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
|
| 542 |
numberOfResults += numberNameResults; |
|
| 543 |
} |
|
| 544 |
} |
|
| 545 |
|
|
| 546 |
// Taxa from common names |
|
| 547 |
|
|
| 548 |
if (configurator.isDoTaxaByCommonNames()) {
|
|
| 549 |
taxa = null; |
|
| 550 |
numberTaxaResults = 0; |
|
| 551 |
if(configurator.getPageSize() != null){// no point counting if we need all anyway
|
|
| 552 |
numberTaxaResults = dao.countTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas()); |
|
| 553 |
} |
|
| 554 |
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){
|
|
| 555 |
taxa = dao.getTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas(), configurator.getPageSize(), configurator.getPageNumber(), configurator.getTaxonPropertyPath()); |
|
| 556 |
} |
|
| 557 |
if(taxa != null){
|
|
| 558 |
results.addAll(taxa); |
|
| 559 |
} |
|
| 560 |
numberOfResults += numberTaxaResults; |
|
| 561 |
|
|
| 562 |
} |
|
| 563 |
|
|
| 564 |
return new DefaultPagerImpl<IdentifiableEntity> |
|
| 565 |
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results); |
|
| 566 |
} |
|
| 567 |
|
|
| 568 |
public List<UuidAndTitleCache<TaxonBase>> getTaxonUuidAndTitleCache(){
|
|
| 569 |
return dao.getUuidAndTitleCache(); |
|
| 570 |
} |
|
| 571 |
|
|
| 572 |
/* (non-Javadoc) |
|
| 573 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllMedia(eu.etaxonomy.cdm.model.taxon.Taxon, int, int, int, java.lang.String[]) |
|
| 574 |
*/ |
|
| 575 |
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){
|
|
| 576 |
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>(); |
|
| 577 |
taxon = (Taxon)dao.load(taxon.getUuid()); |
|
| 578 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
|
| 579 |
for (TaxonDescription taxDesc: descriptions){
|
|
| 580 |
Set<DescriptionElementBase> elements = taxDesc.getElements(); |
|
| 581 |
for (DescriptionElementBase descElem: elements){
|
|
| 582 |
for(Media media : descElem.getMedia()){
|
|
| 583 |
|
|
| 584 |
//find the best matching representation |
|
| 585 |
medRep.add(MediaUtils.findBestMatchingRepresentation(media, null, size, height, widthOrDuration, mimeTypes)); |
|
| 586 |
|
|
| 587 |
} |
|
| 588 |
} |
|
| 589 |
} |
|
| 590 |
return medRep; |
|
| 591 |
} |
|
| 592 |
|
|
| 593 |
/* (non-Javadoc) |
|
| 594 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByID(java.util.Set) |
|
| 595 |
*/ |
|
| 596 |
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {
|
|
| 597 |
return this.dao.findById(listOfIDs); |
|
| 598 |
} |
|
| 599 |
|
|
| 600 |
/* (non-Javadoc) |
|
| 601 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#countAllRelationships() |
|
| 602 |
*/ |
|
| 603 |
public int countAllRelationships() {
|
|
| 604 |
return this.dao.countAllRelationships(); |
|
| 605 |
} |
|
| 606 |
|
|
| 607 |
/* (non-Javadoc) |
|
| 608 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createAllInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon) |
|
| 609 |
*/ |
|
| 610 |
public List<Synonym> createAllInferredSynonyms(Classification tree, |
|
| 611 |
Taxon taxon) {
|
|
| 612 |
|
|
| 613 |
return this.dao.createAllInferredSynonyms(taxon, tree); |
|
| 614 |
} |
|
| 615 |
|
|
| 616 |
/* (non-Javadoc) |
|
| 617 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType) |
|
| 618 |
*/ |
|
| 619 |
public List<Synonym> createInferredSynonyms(Classification tree, Taxon taxon, SynonymRelationshipType type) {
|
|
| 620 |
|
|
| 621 |
return this.dao.createInferredSynonyms(taxon, tree, type); |
|
| 622 |
} |
|
| 623 |
|
|
| 624 |
/* (non-Javadoc) |
|
| 625 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNames(java.util.List) |
|
| 626 |
*/ |
|
| 627 |
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {
|
|
| 628 |
|
|
| 629 |
return this.dao.findIdenticalTaxonNames(propertyPath); |
|
| 630 |
} |
|
| 631 |
|
|
| 632 |
/* (non-Javadoc) |
|
| 633 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List) |
|
| 634 |
*/ |
|
| 635 |
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {
|
|
| 636 |
|
|
| 637 |
return this.dao.findIdenticalNamesNew(propertyPath); |
|
| 638 |
} |
|
| 639 |
|
|
| 640 |
/* (non-Javadoc) |
|
| 641 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getPhylumName(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
|
| 642 |
*/ |
|
| 643 |
public String getPhylumName(TaxonNameBase name){
|
|
| 644 |
return this.dao.getPhylumName(name); |
|
| 645 |
} |
|
| 646 |
|
|
| 647 |
private class TaxonAndNameComparator implements Comparator{
|
|
| 648 |
|
|
| 649 |
public int compare(Object arg0, Object arg1) {
|
|
| 650 |
IdentifiableEntity castArg0 = (IdentifiableEntity) arg0; |
|
| 651 |
IdentifiableEntity castArg1 = (IdentifiableEntity) arg1; |
|
| 652 |
return castArg0.compareTo(castArg1); |
|
| 653 |
} |
|
| 654 |
|
|
| 655 |
} |
|
| 656 |
|
|
| 657 |
/* (non-Javadoc) |
|
| 658 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym) |
|
| 659 |
*/ |
|
| 660 |
public long deleteSynonymRelationships(Synonym syn) {
|
|
| 661 |
|
|
| 662 |
return dao.deleteSynonymRelationships(syn); |
|
| 663 |
} |
|
| 664 |
|
|
| 665 |
|
|
| 666 |
/* (non-Javadoc) |
|
| 667 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listSynonymRelationships(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction) |
|
| 668 |
*/ |
|
| 669 |
public List<SynonymRelationship> listSynonymRelationships( |
|
| 670 |
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, |
|
| 671 |
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {
|
|
| 672 |
Integer numberOfResults = dao.countSynonymRelationships(taxonBase, type, direction); |
|
| 673 |
|
|
| 674 |
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>(); |
|
| 675 |
if(numberOfResults > 0) { // no point checking again
|
|
| 676 |
results = dao.getSynonymRelationships(taxonBase, type, pageSize, pageNumber, orderHints, propertyPaths, direction); |
|
| 677 |
} |
|
| 678 |
return results; |
|
| 679 |
} |
|
| 680 |
|
|
| 681 |
/* (non-Javadoc) |
|
| 682 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingTaxon(java.lang.String) |
|
| 683 |
*/ |
|
| 684 |
@Override |
|
| 685 |
public Taxon findBestMatchingTaxon(String taxonName) {
|
|
| 686 |
MatchingTaxonConfigurator config = MatchingTaxonConfigurator.NewInstance(); |
|
| 687 |
config.setTaxonNameTitle(taxonName); |
|
| 688 |
return findBestMatchingTaxon(config); |
|
| 689 |
} |
|
| 690 |
|
|
| 691 |
|
|
| 692 |
|
|
| 693 |
@Override |
|
| 694 |
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config) {
|
|
| 695 |
|
|
| 696 |
Taxon bestCandidate = null; |
|
| 697 |
try{
|
|
| 698 |
// 1. search for acceptet taxa |
|
| 699 |
List<TaxonBase> taxonList = dao.findByNameTitleCache(Taxon.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null); |
|
| 700 |
boolean bestCandidateMatchesSecUuid = false; |
|
| 701 |
boolean bestCandidateIsInClassification = false; |
|
| 702 |
int countEqualCandidates = 0; |
|
| 703 |
for(TaxonBase taxonBaseCandidate : taxonList){
|
|
| 704 |
if(taxonBaseCandidate instanceof Taxon){
|
|
| 705 |
Taxon newCanditate = CdmBase.deproxy(taxonBaseCandidate, Taxon.class); |
|
| 706 |
boolean newCandidateMatchesSecUuid = isMatchesSecUuid(newCanditate, config); |
|
| 707 |
if (! newCandidateMatchesSecUuid && config.isOnlyMatchingSecUuid() ){
|
|
| 708 |
continue; |
|
| 709 |
}else if(newCandidateMatchesSecUuid && ! bestCandidateMatchesSecUuid){
|
|
| 710 |
bestCandidate = newCanditate; |
|
| 711 |
countEqualCandidates = 1; |
|
| 712 |
bestCandidateMatchesSecUuid = true; |
|
| 713 |
continue; |
|
| 714 |
} |
|
| 715 |
|
|
| 716 |
boolean newCandidateInClassification = isInClassification(newCanditate, config); |
|
| 717 |
if (! newCandidateInClassification && config.isOnlyMatchingClassificationUuid()){
|
|
| 718 |
continue; |
|
| 719 |
}else if (newCandidateInClassification && ! bestCandidateIsInClassification){
|
|
| 720 |
bestCandidate = newCanditate; |
|
| 721 |
countEqualCandidates = 1; |
|
| 722 |
bestCandidateIsInClassification = true; |
|
| 723 |
continue; |
|
| 724 |
} |
|
| 725 |
if (bestCandidate == null){
|
|
| 726 |
bestCandidate = newCanditate; |
|
| 727 |
countEqualCandidates = 1; |
|
| 728 |
continue; |
|
| 729 |
} |
|
| 730 |
|
|
| 731 |
}else{ //not Taxon.class
|
|
| 732 |
continue; |
|
| 733 |
} |
|
| 734 |
countEqualCandidates++; |
|
| 735 |
|
|
| 736 |
} |
|
| 737 |
if (bestCandidate != null){
|
|
| 738 |
if(countEqualCandidates > 1){
|
|
| 739 |
logger.info(countEqualCandidates + " equally matching TaxonBases found, using first accepted Taxon: " + bestCandidate.getTitleCache()); |
|
| 740 |
return bestCandidate; |
|
| 741 |
} else {
|
|
| 742 |
logger.info("using accepted Taxon: " + bestCandidate.getTitleCache());
|
|
| 743 |
return bestCandidate; |
|
| 744 |
} |
|
| 745 |
} |
|
| 746 |
|
|
| 747 |
|
|
| 748 |
// 2. search for synonyms |
|
| 749 |
if (config.isIncludeSynonyms()){
|
|
| 750 |
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null); |
|
| 751 |
for(TaxonBase taxonBase : synonymList){
|
|
| 752 |
if(taxonBase instanceof Synonym){
|
|
| 753 |
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class); |
|
| 754 |
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa(); |
|
| 755 |
if(!acceptetdCandidates.isEmpty()){
|
|
| 756 |
bestCandidate = acceptetdCandidates.iterator().next(); |
|
| 757 |
if(acceptetdCandidates.size() == 1){
|
|
| 758 |
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxonBase.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache()); |
|
| 759 |
return bestCandidate; |
|
| 760 |
} else {
|
|
| 761 |
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxonBase.getTitleCache());
|
|
| 762 |
return bestCandidate; |
|
| 763 |
} |
|
| 764 |
//TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found |
|
| 765 |
} |
|
| 766 |
} |
|
| 767 |
} |
|
| 768 |
} |
|
| 769 |
|
|
| 770 |
} catch (Exception e){
|
|
| 771 |
logger.error(e); |
|
| 772 |
} |
|
| 773 |
|
|
| 774 |
return bestCandidate; |
|
| 775 |
} |
|
| 776 |
|
|
| 777 |
private boolean isInClassification(Taxon taxon, MatchingTaxonConfigurator config) {
|
|
| 778 |
UUID configClassificationUuid = config.getClassificationUuid(); |
|
| 779 |
if (configClassificationUuid == null){
|
|
| 780 |
return false; |
|
| 781 |
} |
|
| 782 |
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
| 783 |
UUID classUuid = node.getClassification().getUuid(); |
|
| 784 |
if (configClassificationUuid.equals(classUuid)){
|
|
| 785 |
return true; |
|
| 786 |
} |
|
| 787 |
} |
|
| 788 |
return false; |
|
| 789 |
} |
|
| 790 |
|
|
| 791 |
private boolean isMatchesSecUuid(Taxon taxon, MatchingTaxonConfigurator config) {
|
|
| 792 |
UUID configSecUuid = config.getSecUuid(); |
|
| 793 |
if (configSecUuid == null){
|
|
| 794 |
return false; |
|
| 795 |
} |
|
| 796 |
UUID taxonSecUuid = (taxon.getSec() == null)? null : taxon.getSec().getUuid(); |
|
| 797 |
return configSecUuid.equals(taxonSecUuid); |
|
| 798 |
} |
|
| 799 |
|
|
| 800 |
/* (non-Javadoc) |
|
| 801 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingSynonym(java.lang.String) |
|
| 802 |
*/ |
|
| 803 |
@Override |
|
| 804 |
public Synonym findBestMatchingSynonym(String taxonName) {
|
|
| 805 |
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, taxonName, null, MatchMode.EXACT, null, 0, null, null); |
|
| 806 |
if(! synonymList.isEmpty()){
|
|
| 807 |
Synonym result = CdmBase.deproxy(synonymList.iterator().next(), Synonym.class); |
|
| 808 |
if(synonymList.size() == 1){
|
|
| 809 |
logger.info(synonymList.size() + " Synonym found " + result.getTitleCache() ); |
|
| 810 |
return result; |
|
| 811 |
} else {
|
|
| 812 |
logger.info("Several matching synonyms found. Using first: " + result.getTitleCache());
|
|
| 813 |
return result; |
|
| 814 |
} |
|
| 815 |
} |
|
| 816 |
return null; |
|
| 817 |
} |
|
| 818 |
|
|
| 819 |
/* (non-Javadoc) |
|
| 820 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#moveSynonymToAnotherTaxon(eu.etaxonomy.cdm.model.taxon.SynonymRelationship, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String) |
|
| 821 |
*/ |
|
| 822 |
@Override |
|
| 823 |
public Taxon moveSynonymToAnotherTaxon(SynonymRelationship synonymRelation, |
|
| 824 |
Taxon toTaxon, SynonymRelationshipType synonymRelationshipType, Reference reference, String referenceDetail) {
|
|
| 825 |
Taxon fromTaxon = synonymRelation.getAcceptedTaxon(); |
|
| 826 |
|
|
| 827 |
toTaxon.addSynonym(synonymRelation.getSynonym(), synonymRelationshipType, reference, referenceDetail); |
|
| 828 |
|
|
| 829 |
fromTaxon.removeSynonymRelation(synonymRelation); |
|
| 830 |
|
|
| 831 |
return toTaxon; |
|
| 832 |
} |
|
| 833 |
|
|
| 834 |
/* (non-Javadoc) |
|
| 835 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheTaxon() |
|
| 836 |
*/ |
|
| 837 |
@Override |
|
| 838 |
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {
|
|
| 839 |
return dao.getUuidAndTitleCacheTaxon(); |
|
| 840 |
} |
|
| 841 |
|
|
| 842 |
/* (non-Javadoc) |
|
| 843 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheSynonym() |
|
| 844 |
*/ |
|
| 845 |
@Override |
|
| 846 |
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {
|
|
| 847 |
return dao.getUuidAndTitleCacheSynonym(); |
|
| 848 |
} |
|
| 849 |
|
|
| 850 |
|
|
| 529 |
|
|
| 530 |
List<? extends TaxonNameBase<?,?>> names = |
|
| 531 |
nameDao.findByName(configurator.getTitleSearchStringSqlized(), configurator.getMatchMode(), |
|
| 532 |
configurator.getPageSize(), configurator.getPageNumber(), null, configurator.getTaxonNamePropertyPath()); |
|
| 533 |
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
|
| 534 |
if (names.size() > 0) {
|
|
| 535 |
for (TaxonNameBase<?,?> taxonName : names) {
|
|
| 536 |
if (taxonName.getTaxonBases().size() == 0) {
|
|
| 537 |
results.add(taxonName); |
|
| 538 |
numberNameResults++; |
|
| 539 |
} |
|
| 540 |
} |
|
| 541 |
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
|
| 542 |
numberOfResults += numberNameResults; |
|
| 543 |
} |
|
| 544 |
} |
|
| 545 |
|
|
| 546 |
// Taxa from common names |
|
| 547 |
|
|
| 548 |
if (configurator.isDoTaxaByCommonNames()) {
|
|
| 549 |
taxa = null; |
|
| 550 |
numberTaxaResults = 0; |
|
| 551 |
if(configurator.getPageSize() != null){// no point counting if we need all anyway
|
|
| 552 |
numberTaxaResults = dao.countTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas()); |
|
| 553 |
} |
|
| 554 |
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){
|
|
| 555 |
taxa = dao.getTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas(), configurator.getPageSize(), configurator.getPageNumber(), configurator.getTaxonPropertyPath()); |
|
| 556 |
} |
|
| 557 |
if(taxa != null){
|
|
| 558 |
results.addAll(taxa); |
|
| 559 |
} |
|
| 560 |
numberOfResults += numberTaxaResults; |
|
| 561 |
|
|
| 562 |
} |
|
| 563 |
|
|
| 564 |
return new DefaultPagerImpl<IdentifiableEntity> |
|
| 565 |
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results); |
|
| 566 |
} |
|
| 567 |
|
|
| 568 |
public List<UuidAndTitleCache<TaxonBase>> getTaxonUuidAndTitleCache(){
|
|
| 569 |
return dao.getUuidAndTitleCache(); |
|
| 570 |
} |
|
| 571 |
|
|
| 572 |
/* (non-Javadoc) |
|
| 573 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllMedia(eu.etaxonomy.cdm.model.taxon.Taxon, int, int, int, java.lang.String[]) |
|
| 574 |
*/ |
|
| 575 |
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){
|
|
| 576 |
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>(); |
|
| 577 |
taxon = (Taxon)dao.load(taxon.getUuid()); |
|
| 578 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
|
| 579 |
for (TaxonDescription taxDesc: descriptions){
|
|
| 580 |
Set<DescriptionElementBase> elements = taxDesc.getElements(); |
|
| 581 |
for (DescriptionElementBase descElem: elements){
|
|
| 582 |
for(Media media : descElem.getMedia()){
|
|
| 583 |
|
|
| 584 |
//find the best matching representation |
|
| 585 |
medRep.add(MediaUtils.findBestMatchingRepresentation(media, null, size, height, widthOrDuration, mimeTypes)); |
|
| 586 |
|
|
| 587 |
} |
|
| 588 |
} |
|
| 589 |
} |
|
| 590 |
return medRep; |
|
| 591 |
} |
|
| 592 |
|
|
| 593 |
/* (non-Javadoc) |
|
| 594 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByID(java.util.Set) |
|
| 595 |
*/ |
|
| 596 |
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {
|
|
| 597 |
return this.dao.findById(listOfIDs); |
|
| 598 |
} |
|
| 599 |
|
|
| 600 |
/* (non-Javadoc) |
|
| 601 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#countAllRelationships() |
|
| 602 |
*/ |
|
| 603 |
public int countAllRelationships() {
|
|
| 604 |
return this.dao.countAllRelationships(); |
|
| 605 |
} |
|
| 606 |
|
|
| 607 |
/* (non-Javadoc) |
|
| 608 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createAllInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon) |
|
| 609 |
*/ |
|
| 610 |
public List<Synonym> createAllInferredSynonyms(Classification tree, |
|
| 611 |
Taxon taxon) {
|
|
| 612 |
|
|
| 613 |
return this.dao.createAllInferredSynonyms(taxon, tree); |
|
| 614 |
} |
|
| 615 |
|
|
| 616 |
/* (non-Javadoc) |
|
| 617 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType) |
|
| 618 |
*/ |
|
| 619 |
public List<Synonym> createInferredSynonyms(Classification tree, Taxon taxon, SynonymRelationshipType type) {
|
|
| 620 |
|
|
| 621 |
return this.dao.createInferredSynonyms(taxon, tree, type); |
|
| 622 |
} |
|
| 623 |
|
|
| 624 |
/* (non-Javadoc) |
|
| 625 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNames(java.util.List) |
|
| 626 |
*/ |
|
| 627 |
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {
|
|
| 628 |
|
|
| 629 |
return this.dao.findIdenticalTaxonNames(propertyPath); |
|
| 630 |
} |
|
| 631 |
|
|
| 632 |
/* (non-Javadoc) |
|
| 633 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List) |
|
| 634 |
*/ |
|
| 635 |
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {
|
|
| 636 |
|
|
| 637 |
return this.dao.findIdenticalNamesNew(propertyPath); |
|
| 638 |
} |
|
| 639 |
|
|
| 640 |
/* (non-Javadoc) |
|
| 641 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getPhylumName(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
|
| 642 |
*/ |
|
| 643 |
public String getPhylumName(TaxonNameBase name){
|
|
| 644 |
return this.dao.getPhylumName(name); |
|
| 645 |
} |
|
| 646 |
|
|
| 647 |
/* (non-Javadoc) |
|
| 648 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym) |
|
| 649 |
*/ |
|
| 650 |
public long deleteSynonymRelationships(Synonym syn) {
|
|
| 651 |
|
|
| 652 |
return dao.deleteSynonymRelationships(syn); |
|
| 653 |
} |
|
| 654 |
|
|
| 655 |
|
|
| 656 |
/* (non-Javadoc) |
|
| 657 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listSynonymRelationships(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction) |
|
| 658 |
*/ |
|
| 659 |
public List<SynonymRelationship> listSynonymRelationships( |
|
| 660 |
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, |
|
| 661 |
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {
|
|
| 662 |
Integer numberOfResults = dao.countSynonymRelationships(taxonBase, type, direction); |
|
| 663 |
|
|
| 664 |
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>(); |
|
| 665 |
if(numberOfResults > 0) { // no point checking again
|
|
| 666 |
results = dao.getSynonymRelationships(taxonBase, type, pageSize, pageNumber, orderHints, propertyPaths, direction); |
|
| 667 |
} |
|
| 668 |
return results; |
|
| 669 |
} |
|
| 670 |
|
|
| 671 |
/* (non-Javadoc) |
|
| 672 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingTaxon(java.lang.String) |
|
| 673 |
*/ |
|
| 674 |
@Override |
|
| 675 |
public Taxon findBestMatchingTaxon(String taxonName) {
|
|
| 676 |
MatchingTaxonConfigurator config = MatchingTaxonConfigurator.NewInstance(); |
|
| 677 |
config.setTaxonNameTitle(taxonName); |
|
| 678 |
return findBestMatchingTaxon(config); |
|
| 679 |
} |
|
| 680 |
|
|
| 681 |
|
|
| 682 |
|
|
| 683 |
@Override |
|
| 684 |
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config) {
|
|
| 685 |
|
|
| 686 |
Taxon bestCandidate = null; |
|
| 687 |
try{
|
|
| 688 |
// 1. search for acceptet taxa |
|
| 689 |
List<TaxonBase> taxonList = dao.findByNameTitleCache(Taxon.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null); |
|
| 690 |
boolean bestCandidateMatchesSecUuid = false; |
|
| 691 |
boolean bestCandidateIsInClassification = false; |
|
| 692 |
int countEqualCandidates = 0; |
|
| 693 |
for(TaxonBase taxonBaseCandidate : taxonList){
|
|
| 694 |
if(taxonBaseCandidate instanceof Taxon){
|
|
| 695 |
Taxon newCanditate = CdmBase.deproxy(taxonBaseCandidate, Taxon.class); |
|
| 696 |
boolean newCandidateMatchesSecUuid = isMatchesSecUuid(newCanditate, config); |
|
| 697 |
if (! newCandidateMatchesSecUuid && config.isOnlyMatchingSecUuid() ){
|
|
| 698 |
continue; |
|
| 699 |
}else if(newCandidateMatchesSecUuid && ! bestCandidateMatchesSecUuid){
|
|
| 700 |
bestCandidate = newCanditate; |
|
| 701 |
countEqualCandidates = 1; |
|
| 702 |
bestCandidateMatchesSecUuid = true; |
|
| 703 |
continue; |
|
| 704 |
} |
|
| 705 |
|
|
| 706 |
boolean newCandidateInClassification = isInClassification(newCanditate, config); |
|
| 707 |
if (! newCandidateInClassification && config.isOnlyMatchingClassificationUuid()){
|
|
| 708 |
continue; |
|
| 709 |
}else if (newCandidateInClassification && ! bestCandidateIsInClassification){
|
|
| 710 |
bestCandidate = newCanditate; |
|
| 711 |
countEqualCandidates = 1; |
|
| 712 |
bestCandidateIsInClassification = true; |
|
| 713 |
continue; |
|
| 714 |
} |
|
| 715 |
if (bestCandidate == null){
|
|
| 716 |
bestCandidate = newCanditate; |
|
| 717 |
countEqualCandidates = 1; |
|
| 718 |
continue; |
|
| 719 |
} |
|
| 720 |
|
|
| 721 |
}else{ //not Taxon.class
|
|
| 722 |
continue; |
|
| 723 |
} |
|
| 724 |
countEqualCandidates++; |
|
| 725 |
|
|
| 726 |
} |
|
| 727 |
if (bestCandidate != null){
|
|
| 728 |
if(countEqualCandidates > 1){
|
|
| 729 |
logger.info(countEqualCandidates + " equally matching TaxonBases found, using first accepted Taxon: " + bestCandidate.getTitleCache()); |
|
| 730 |
return bestCandidate; |
|
| 731 |
} else {
|
|
| 732 |
logger.info("using accepted Taxon: " + bestCandidate.getTitleCache());
|
|
| 733 |
return bestCandidate; |
|
| 734 |
} |
|
| 735 |
} |
|
| 736 |
|
|
| 737 |
|
|
| 738 |
// 2. search for synonyms |
|
| 739 |
if (config.isIncludeSynonyms()){
|
|
| 740 |
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null); |
|
| 741 |
for(TaxonBase taxonBase : synonymList){
|
|
| 742 |
if(taxonBase instanceof Synonym){
|
|
| 743 |
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class); |
|
| 744 |
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa(); |
|
| 745 |
if(!acceptetdCandidates.isEmpty()){
|
|
| 746 |
bestCandidate = acceptetdCandidates.iterator().next(); |
|
| 747 |
if(acceptetdCandidates.size() == 1){
|
|
| 748 |
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxonBase.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache()); |
|
| 749 |
return bestCandidate; |
|
| 750 |
} else {
|
|
| 751 |
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxonBase.getTitleCache());
|
|
| 752 |
return bestCandidate; |
|
| 753 |
} |
|
| 754 |
//TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found |
|
| 755 |
} |
|
| 756 |
} |
|
| 757 |
} |
|
| 758 |
} |
|
| 759 |
|
|
| 760 |
} catch (Exception e){
|
|
| 761 |
logger.error(e); |
|
| 762 |
} |
|
| 763 |
|
|
| 764 |
return bestCandidate; |
|
| 765 |
} |
|
| 766 |
|
|
| 767 |
private boolean isInClassification(Taxon taxon, MatchingTaxonConfigurator config) {
|
|
| 768 |
UUID configClassificationUuid = config.getClassificationUuid(); |
|
| 769 |
if (configClassificationUuid == null){
|
|
| 770 |
return false; |
|
| 771 |
} |
|
| 772 |
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
| 773 |
UUID classUuid = node.getClassification().getUuid(); |
|
Also available in: Unified diff
removing unused private class TaxonAndNameComparator