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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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* 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.remote.service;
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import java.util.ArrayList;
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import java.util.Enumeration;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.Locale;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.criterion.Criterion;
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import org.hibernate.criterion.Restrictions;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.IReferenceService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IFeatureDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IFeatureTreeDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.remote.dto.FeatureTO;
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import eu.etaxonomy.cdm.remote.dto.FeatureTreeTO;
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import eu.etaxonomy.cdm.remote.dto.NameSTO;
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import eu.etaxonomy.cdm.remote.dto.NameTO;
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import eu.etaxonomy.cdm.remote.dto.ReferenceSTO;
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import eu.etaxonomy.cdm.remote.dto.ReferencedEntityBaseSTO;
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import eu.etaxonomy.cdm.remote.dto.ResultSetPageSTO;
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import eu.etaxonomy.cdm.remote.dto.TaxonSTO;
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import eu.etaxonomy.cdm.remote.dto.TaxonTO;
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import eu.etaxonomy.cdm.remote.dto.TreeNode;
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import eu.etaxonomy.cdm.remote.dto.assembler.AnnotationAssembler;
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import eu.etaxonomy.cdm.remote.dto.assembler.DescriptionAssembler;
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import eu.etaxonomy.cdm.remote.dto.assembler.NameAssembler;
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import eu.etaxonomy.cdm.remote.dto.assembler.ReferenceAssembler;
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import eu.etaxonomy.cdm.remote.dto.assembler.TaxonAssembler;
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@Service
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@Transactional(readOnly = true)
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public class CdmServiceImpl implements ICdmService {
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static Logger logger = Logger.getLogger(CdmServiceImpl.class);
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@Autowired
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private ReferenceAssembler refAssembler;
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@Autowired
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private NameAssembler nameAssembler;
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@Autowired
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private TaxonAssembler taxonAssembler;
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@Autowired
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private DescriptionAssembler descriptionAssembler;
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@Autowired
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private AnnotationAssembler annotationAssembler;
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@Autowired
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private ITaxonDao taxonDAO;
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@Autowired
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private ITaxonNameDao nameDAO;
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@Autowired
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private IReferenceDao refDAO;
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@Autowired
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private IDescriptionDao descriptionDAO;
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@Autowired
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private IFeatureTreeDao featureTreeDAO;
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@Autowired
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private IFeatureDao featureDAO;
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//FIXME commented out below, since refactoring is urgently needed see ticket#593 http://dev.e-taxonomy.eu/trac/ticket/593
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// @Autowired
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// private AnnotatableDaoImpl<AnnotatableEntity> annotatableDao;
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//--------------------------
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@Autowired
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private IReferenceService referenceService;
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private final int MAXRESULTS = 500;
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private static List<OrderHint> defaultReferenceOrder = new ArrayList();
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// private CdmEntityDaoBase entityDAO = new CdmEntityDaoBase<CdmBase>();
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public CdmServiceImpl() {
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super();
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defaultReferenceOrder.add(new OrderHint("authorTeam.persistentTitleCache", OrderHint.SortOrder.ASCENDING));
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defaultReferenceOrder.add(new OrderHint("year", OrderHint.SortOrder.ASCENDING));
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defaultReferenceOrder.add(new OrderHint("persistentTitleCache", OrderHint.SortOrder.ASCENDING));
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}
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/**
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* find matching taxonbase instance or throw CdmObjectNonExisting exception.
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* never returns null!
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* @param uuid
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* @return
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* @throws CdmObjectNonExisting
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*/
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private TaxonBase getCdmTaxonBase(UUID uuid) throws CdmObjectNonExisting{
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TaxonBase tb = taxonDAO.findByUuid(uuid);
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if (tb==null){
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throw new CdmObjectNonExisting(uuid.toString(), TaxonBase.class);
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}
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return tb;
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}
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private Taxon getCdmTaxon(UUID uuid) throws CdmObjectNonExisting{
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Taxon t = null;
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try {
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t = (Taxon) getCdmTaxonBase(uuid);
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} catch (ClassCastException e) {
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throw new CdmObjectNonExisting(uuid.toString(), Taxon.class);
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}
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return t;
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}
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private TaxonNameBase getCdmTaxonNameBase(UUID uuid) throws CdmObjectNonExisting{
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TaxonNameBase tnb = nameDAO.findByUuid(uuid);
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if (tnb==null){
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throw new CdmObjectNonExisting(uuid.toString(), TaxonNameBase.class);
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}
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return tnb;
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}
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private ReferenceBase getCdmReferenceBase(UUID uuid) throws CdmObjectNonExisting{
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ReferenceBase ref = refDAO.findByUuid(uuid);
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if (ref==null){
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throw new CdmObjectNonExisting(uuid.toString(), ReferenceBase.class);
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}
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return ref;
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}
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public NameTO getName(UUID uuid, Enumeration<Locale> locales) throws CdmObjectNonExisting{
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TaxonNameBase tnb = getCdmTaxonNameBase(uuid);
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NameTO n = nameAssembler.getTO(tnb, locales);
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return n;
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}
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public NameSTO getSimpleName(UUID uuid, Enumeration<Locale> locales) throws CdmObjectNonExisting{
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TaxonNameBase tnb = getCdmTaxonNameBase(uuid);
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NameSTO n = nameAssembler.getSTO(tnb, locales);
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return n;
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}
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public TaxonTO getTaxon(UUID taxonUuid, UUID featureTreeUuid, Enumeration<Locale> locales) throws CdmObjectNonExisting{
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TaxonBase tb = taxonDAO.findByUuid(taxonUuid);
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if (tb==null){
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throw new CdmObjectNonExisting(taxonUuid.toString(), TaxonBase.class);
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}
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FeatureTree featureTree = null;
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if (featureTreeUuid != null){
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featureTree = featureTreeDAO.findByUuid(featureTreeUuid);
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if (featureTree == null){
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throw new CdmObjectNonExisting(featureTreeUuid.toString(), FeatureTree.class);
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}
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}else{
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logger.info("No featureTree at this point. Building default tree with all available features.");
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featureTree = FeatureTree.NewInstance(featureDAO.list());
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}
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TaxonTO t = taxonAssembler.getTO(tb, featureTree, locales);
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return t;
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}
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public TaxonSTO getSimpleTaxon(UUID uuid, Enumeration<Locale> locales) throws CdmObjectNonExisting{
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TaxonBase tb = getCdmTaxonBase(uuid);
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TaxonSTO t = taxonAssembler.getSTO(tb, locales);
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return t;
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}
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public Class whatis(UUID uuid) throws CdmObjectNonExisting{
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//CdmBase cb = entityDAO.findByUuid(uuid);
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return this.getClass();
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}
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public ResultSetPageSTO<TaxonSTO> findTaxa(String q, Set<UUID> sec, Set<UUID> higherTaxa, MatchMode matchMode, boolean onlyAccepted, int page, int pagesize, Enumeration<Locale> locales) {
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ResultSetPageSTO<TaxonSTO> resultSetPage = new ResultSetPageSTO<TaxonSTO>();
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resultSetPage.setPageNumber(page);
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resultSetPage.setPageSize(pagesize);
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// TODO: add other criteria. Has to be done in DAO...
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List<Criterion> criteria = new ArrayList<Criterion>();
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if(sec.size()>0){
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List<ReferenceBase> secundum = new ArrayList<ReferenceBase>();
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for (UUID uuid : sec){
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ReferenceBase referenceBase = refDAO.findByUuid(uuid);
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secundum.add(referenceBase);
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}
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criteria.add(Restrictions.in("sec", secundum));
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}
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resultSetPage.setTotalResultsCount((int)taxonDAO.countMatchesByName(q, matchMode, onlyAccepted, criteria));
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// if(MAXRESULTS > 0 && rs.getTotalResultsCount() > MAXRESULTS){
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// rs.setTotalResultsCount(-1);
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// return rs;
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// }
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List<TaxonBase> results = taxonDAO.findByTitle(q, matchMode, page, pagesize, criteria);
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//descriptionDAO
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resultSetPage.setResultsOnPage(results.size());
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for (TaxonBase taxonBase : results){
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resultSetPage.getResults().add(taxonAssembler.getSTO(taxonBase, locales));
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}
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return resultSetPage;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.remote.service.ICdmService#getAcceptedTaxon(java.util.Set, java.util.Enumeration)
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*/
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public Hashtable<String, List<TaxonSTO>> getAcceptedTaxa(Set<UUID> uuids, Enumeration<Locale> locales) throws CdmObjectNonExisting {
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Hashtable<String, List<TaxonSTO>> stoTable = new Hashtable<String, List<TaxonSTO>>();
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for (UUID uuid : uuids) {
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List<TaxonSTO> stoList = new ArrayList<TaxonSTO>();
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TaxonBase tb = getCdmTaxonBase(uuid);
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if (tb.getClass().equals(Taxon.class)){
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TaxonSTO t = taxonAssembler.getSTO(tb, locales);
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stoList.add(t);
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}else{
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Synonym s = (Synonym)tb;
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Set<Taxon> taxa = s.getAcceptedTaxa();
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for (Taxon tx: taxa){
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TaxonSTO t = taxonAssembler.getSTO(tx, locales);
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stoList.add(t);
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}
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}
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stoTable.put(uuid.toString(), stoList);
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}
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return stoTable;
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}
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public List<TreeNode> getChildTaxa(UUID uuid) throws CdmObjectNonExisting {
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Taxon tx = getCdmTaxon(uuid);
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return taxonAssembler.getTreeNodeListSortedByName(tx.getTaxonomicChildren());
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}
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public List<TreeNode> getParentTaxa(UUID uuid) throws CdmObjectNonExisting {
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ArrayList<TreeNode> result = new ArrayList<TreeNode>();
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Taxon tx = getCdmTaxon(uuid);
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result.add(taxonAssembler.getTreeNode(tx));
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while(tx.getTaxonomicParent() != null){
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Taxon parent = tx.getTaxonomicParent();
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result.add(taxonAssembler.getTreeNode(parent));
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tx=parent;
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}
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return result;
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}
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public ReferenceBase getReference(UUID uuid, Enumeration<Locale> locales) throws CdmObjectNonExisting{
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/*ReferenceBase ref = getCdmReferenceBase(uuid);
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ReferenceTO r = refAssembler.getTO(ref, locales); */
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ReferenceBase r = referenceService.getReferenceByUuid(uuid);
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/* Initialise required collections .. */
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return r;
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}
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public Pager<ReferenceBase> listReferences(Integer pageSize, Integer pageNumber) throws CdmObjectNonExisting {
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return referenceService.getAllReferences(pageSize, pageNumber, defaultReferenceOrder);
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}
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public ReferenceSTO getSimpleReference(UUID uuid, Enumeration<Locale> locales) throws CdmObjectNonExisting{
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ReferenceBase ref = getCdmReferenceBase(uuid);
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ReferenceSTO r = refAssembler.getSTO(ref, locales);
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return r;
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}
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public List<TreeNode> getRootTaxa(UUID uuid) throws CdmObjectNonExisting {
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ReferenceBase sec = null;
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if(uuid != null){
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sec = getCdmReferenceBase(uuid);
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}
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List<Taxon> rt = taxonDAO.getRootTaxa(Rank.GENUS(), sec, null, true, false);
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return taxonAssembler.getTreeNodeListSortedByName(rt);
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}
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public Set<ReferencedEntityBaseSTO> getTypes(UUID uuid) {
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// TODO Auto-generated method stub
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return null;
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}
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@Transactional(readOnly = false)
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public void saveTaxon(Taxon t){
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taxonDAO.save(t);
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}
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public ResultSetPageSTO<TaxonSTO> getAternativeTaxa(UUID uuid, Enumeration<Locale> locales)
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throws CdmObjectNonExisting {
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// TODO Auto-generated method stub
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return null;
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}
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public List<NameSTO> getSimpleNames(Set<UUID> uuids, Enumeration<Locale> locales){
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List<NameSTO> nameList = new ArrayList<NameSTO>();
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for (UUID u: uuids){
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try {
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nameList.add(getSimpleName(u, locales));
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} catch (CdmObjectNonExisting e) {
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logger.warn("Name UUID "+u+" does not exist!");
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}
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}
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return nameList;
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}
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public List<ReferenceSTO> getSimpleReferences(Set<UUID> uuids, Enumeration<Locale> locales) {
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List<ReferenceSTO> refList = new ArrayList<ReferenceSTO>();
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for (UUID u: uuids){
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try {
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refList.add(getSimpleReference(u,locales));
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} catch (CdmObjectNonExisting e) {
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logger.warn("Reference UUID "+u+" does not exist!");
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}
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}
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return refList;
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}
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339
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public List<TaxonSTO> getSimpleTaxa(Set<UUID> uuids, Enumeration<Locale> locales){
|
|
340
|
List<TaxonSTO> taxList = new ArrayList<TaxonSTO>();
|
|
341
|
for (UUID u: uuids){
|
|
342
|
try {
|
|
343
|
taxList.add(getSimpleTaxon(u,locales));
|
|
344
|
} catch (CdmObjectNonExisting e) {
|
|
345
|
logger.warn("Taxon UUID "+u+" does not exist!");
|
|
346
|
}
|
|
347
|
}
|
|
348
|
return taxList;
|
|
349
|
}
|
|
350
|
public List<FeatureTO> getFeatures(Enumeration<Locale> locales) throws CdmObjectNonExisting {
|
|
351
|
List<FeatureTO> featureList = new ArrayList<FeatureTO>();
|
|
352
|
|
|
353
|
for (Feature feature : featureDAO.list()){
|
|
354
|
featureList.add(descriptionAssembler.getTO(feature, locales));
|
|
355
|
}
|
|
356
|
|
|
357
|
return featureList;
|
|
358
|
}
|
|
359
|
public List<FeatureTreeTO> getFeatureTrees(Enumeration<Locale> locales)
|
|
360
|
throws CdmObjectNonExisting {
|
|
361
|
List<FeatureTreeTO> featureTreeList = new ArrayList<FeatureTreeTO>();
|
|
362
|
|
|
363
|
for (FeatureTree featureTree : featureTreeDAO.list()){
|
|
364
|
featureTreeList.add(descriptionAssembler.getTO(featureTree, locales));
|
|
365
|
}
|
|
366
|
|
|
367
|
return featureTreeList;
|
|
368
|
}
|
|
369
|
|
|
370
|
//FIXME commented out below, since refactoring is urgently needed see ticket#593 http://dev.e-taxonomy.eu/trac/ticket/593
|
|
371
|
// /* (non-Javadoc)
|
|
372
|
// * @see eu.etaxonomy.cdm.remote.service.ICdmService#getAnnotations(java.util.UUID)
|
|
373
|
// */
|
|
374
|
// public AnnotationTO getAnnotation(UUID uuid, Enumeration<Locale> locales)
|
|
375
|
// throws CdmObjectNonExisting {
|
|
376
|
// List<AnnotationTO> annotationList = new ArrayList<AnnotationTO>();
|
|
377
|
//
|
|
378
|
// // TODO the cast should be removed, but i (niels) don't know how at the moment
|
|
379
|
// AnnotatableEntity annotatableEntity = (AnnotatableEntity) annotatableDao.findByUuid(uuid);
|
|
380
|
//
|
|
381
|
//
|
|
382
|
// return annotationAssembler.getTO(annotatableEntity, locales);
|
|
383
|
// }
|
|
384
|
// /* (non-Javadoc)
|
|
385
|
// * @see eu.etaxonomy.cdm.remote.service.ICdmService#saveAnnotation(java.util.UUID, eu.etaxonomy.cdm.model.common.Annotation)
|
|
386
|
// */
|
|
387
|
// @Transactional(readOnly=false)
|
|
388
|
// public UUID saveAnnotation(UUID uuid, Annotation annotation)
|
|
389
|
// throws CdmObjectNonExisting {
|
|
390
|
//
|
|
391
|
// AnnotatableEntity annotatableEntity = (AnnotatableEntity) annotatableDao.findByUuid(uuid);
|
|
392
|
//
|
|
393
|
// annotatableEntity.addAnnotation(annotation);
|
|
394
|
//
|
|
395
|
// UUID updatedUuid = annotatableDao.saveOrUpdate(annotatableEntity);
|
|
396
|
// annotatableDao.flush();
|
|
397
|
//
|
|
398
|
// return updatedUuid;
|
|
399
|
// }
|
|
400
|
}
|