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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.io.specimen;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ISourceable;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author p.kelbert
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* @created 20.10.2008
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*/
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public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends SpecimenImportStateBase>
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extends CdmImportBase<CONFIG, STATE> {
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private static final long serialVersionUID = 4423065367998125678L;
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private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
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protected static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
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private static final String COLON = ":";
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@Override
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protected abstract void doInvoke(STATE state);
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/**
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* Handle a single unit
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* @param state
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* @param item
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*/
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protected abstract void handleSingleUnit(STATE state, Object item) ;
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protected TaxonName getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
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TaxonName taxonName = null;
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SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
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//check atomised name data for rank
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//new name will be created
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TaxonName atomisedTaxonName = null;
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if (rank==null && unitIndexInAbcdFile>=0 && ((state.getDataHolder().getAtomisedIdentificationList() != null && !state.getDataHolder().getAtomisedIdentificationList().isEmpty())|| state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
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atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state);
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if(atomisedTaxonName!=null){
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rank = atomisedTaxonName.getRank();
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}
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}
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if(config.isReuseExistingTaxaWhenPossible()){
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TaxonName parsedName = atomisedTaxonName;
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if(parsedName==null){
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parsedName = parseScientificName(scientificName, state, state.getReport(), rank);
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}
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atomisedTaxonName = parsedName;
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if(config.isIgnoreAuthorship() && parsedName!=null){// && preferredFlag){
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// do not ignore authorship for non-preferred names because they need
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// to be created for the determination history
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String nameCache = TaxonName.castAndDeproxy(parsedName).getNameCache();
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List<TaxonName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
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if (!names.isEmpty()){
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taxonName = getBestMatchingName(scientificName, new ArrayList<>(names), state);
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}
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if (taxonName == null && !names.isEmpty()){
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taxonName = names.get(0);
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}
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} else {
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//search for existing names
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List<TaxonName> names = getNameService().listByTitle(TaxonName.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
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taxonName = getBestMatchingName(scientificName, names, state);
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//still nothing found -> try with the atomised name full title cache
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if(taxonName==null && atomisedTaxonName!=null){
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names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
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taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
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//still nothing found -> try with the atomised name title cache
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if(taxonName==null){
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names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
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taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
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}
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}
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}
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}
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if(taxonName==null && atomisedTaxonName!=null){
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taxonName = atomisedTaxonName;
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state.getReport().addName(taxonName);
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logger.info("Created new taxon name "+taxonName);
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if(taxonName.hasProblem()){
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state.getReport().addInfoMessage(String.format("Created %s with parsing problems", taxonName));
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}
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if(!atomisedTaxonName.getTitleCache().equals(scientificName)){
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state.getReport().addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
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}
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}
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else if(taxonName==null){
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//create new taxon name
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if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP)){
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taxonName = TaxonNameFactory.NewBotanicalInstance(rank);
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}else if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN)){
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taxonName = TaxonNameFactory.NewZoologicalInstance(rank);
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}else{
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taxonName = TaxonNameFactory.NewNonViralInstance(rank);
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}
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taxonName.setFullTitleCache(scientificName,true);
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taxonName.setTitleCache(scientificName, true);
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state.getReport().addName(taxonName);
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logger.info("Created new taxon name "+taxonName);
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}
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save(taxonName, state);
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return taxonName;
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}
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protected TaxonName getBestMatchingName(String scientificName, java.util.Collection<TaxonName> names, STATE state){
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Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
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List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
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for (TaxonName name : names) {
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if(!name.getTaxa().isEmpty()){
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Set<Taxon> taxa = name.getTaxa();
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for (Taxon taxon:taxa){
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if (!taxon.getTaxonNodes().isEmpty()){
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//use only taxa included in a classification
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for (TaxonNode node:taxon.getTaxonNodes()){
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if (state.getClassification() != null && node.getClassification().equals(state.getClassification())){
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namesWithAcceptedTaxaInClassification.add(name);
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}else {
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namesWithAcceptedTaxa.add(name);
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}
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}
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}
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}
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}
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}
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String message = String.format("More than one taxon name was found for %s, maybe in other classifications!", scientificName);
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//check for names with accepted taxa in classification
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if(namesWithAcceptedTaxaInClassification.size()>0){
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if(namesWithAcceptedTaxaInClassification.size()>1){
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state.getReport().addInfoMessage(message);
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logger.warn(message);
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return null;
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}
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return namesWithAcceptedTaxaInClassification.iterator().next();
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}
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//check for any names with accepted taxa
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if(namesWithAcceptedTaxa.size()>0){
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if(namesWithAcceptedTaxa.size()>1){
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state.getReport().addInfoMessage(message);
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logger.warn(message);
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return null;
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}
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return namesWithAcceptedTaxa.iterator().next();
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}
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//no names with accepted taxa found -> check accepted taxa of synonyms
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List<Taxon> taxaFromSynonyms = new ArrayList<>();
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for (TaxonName name : names) {
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Set<TaxonBase> taxonBases = name.getTaxonBases();
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for (TaxonBase taxonBase : taxonBases) {
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if(taxonBase.isInstanceOf(Synonym.class)){
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Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
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taxaFromSynonyms.add(synonym.getAcceptedTaxon());
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}
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}
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}
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if(taxaFromSynonyms.size()>0){
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if(taxaFromSynonyms.size()>1){
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state.getReport().addInfoMessage(message);
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logger.warn(message);
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return null;
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}
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return taxaFromSynonyms.iterator().next().getName();
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}
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//no accepted and no synonyms -> return one of the names and create a new taxon
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if (names.isEmpty()){
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return null;
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}else{
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return names.iterator().next();
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}
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}
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/**
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* Parse automatically the scientific name
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* @param scientificName the scientific name to parse
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* @param state the current import state
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* @param report the import report
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* @return a parsed name
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*/
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protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
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NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
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TaxonName taxonName = null;
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boolean problem = false;
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if (logger.isDebugEnabled()){
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logger.debug("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
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}
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if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
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if (taxonName.hasProblem()) {
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problem = true;
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}
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}
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else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
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if (taxonName.hasProblem()) {
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problem = true;
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}
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}
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else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank);
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if (taxonName.hasProblem()) {
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problem = true;
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}
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}
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else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
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if (taxonName.hasProblem()) {
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problem = true;
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}
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}
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if (problem) {
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String message = String.format("Parsing problems for %s", scientificName);
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if(taxonName!=null){
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for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
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message += "\n\t- "+parserProblem;
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}
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}
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report.addInfoMessage(message);
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logger.info(message);
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}
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return taxonName;
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}
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/**
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* Create the name without automatic parsing, either because it failed, or because the user deactivated it.
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* The name is built upon the ABCD fields
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* @param atomisedMap : the ABCD atomised fields
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* @param fullName : the full scientific name
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* @param state
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* @return the corresponding Botanical or Zoological or... name
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*/
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protected TaxonName setTaxonNameByType(
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HashMap<String, String> atomisedMap, String fullName, STATE state) {
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boolean problem = false;
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if (logger.isDebugEnabled()){
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logger.debug("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
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}
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if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
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TaxonName taxonName = TaxonNameFactory.NewZoologicalInstance(null);
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taxonName.setFullTitleCache(fullName, true);
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taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
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taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
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326
|
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
|
|
327
|
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
|
|
328
|
|
|
329
|
if (taxonName.getGenusOrUninomial() != null){
|
|
330
|
taxonName.setRank(Rank.GENUS());
|
|
331
|
}
|
|
332
|
|
|
333
|
if (taxonName.getInfraGenericEpithet() != null){
|
|
334
|
taxonName.setRank(Rank.SUBGENUS());
|
|
335
|
}
|
|
336
|
|
|
337
|
if (taxonName.getSpecificEpithet() != null){
|
|
338
|
taxonName.setRank(Rank.SPECIES());
|
|
339
|
}
|
|
340
|
|
|
341
|
if (taxonName.getInfraSpecificEpithet() != null){
|
|
342
|
taxonName.setRank(Rank.SUBSPECIES());
|
|
343
|
}
|
|
344
|
|
|
345
|
Team team = null;
|
|
346
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
347
|
team = Team.NewInstance();
|
|
348
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
|
|
349
|
}
|
|
350
|
else {
|
|
351
|
if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
|
|
352
|
team = Team.NewInstance();
|
|
353
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
|
|
354
|
}
|
|
355
|
}
|
|
356
|
if (team != null) {
|
|
357
|
taxonName.setBasionymAuthorship(team);
|
|
358
|
}
|
|
359
|
else {
|
|
360
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
361
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
|
|
362
|
}
|
|
363
|
else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
|
|
364
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
|
|
365
|
}
|
|
366
|
}
|
|
367
|
if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
|
|
368
|
team = Team.NewInstance();
|
|
369
|
team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
|
|
370
|
taxonName.setCombinationAuthorship(team);
|
|
371
|
}
|
|
372
|
if (taxonName.hasProblem()) {
|
|
373
|
logger.info("pb ICZN");
|
|
374
|
problem = true;
|
|
375
|
}
|
|
376
|
else {
|
|
377
|
return taxonName;
|
|
378
|
}
|
|
379
|
}
|
|
380
|
else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
|
|
381
|
TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null);
|
|
382
|
if (taxonName != null){
|
|
383
|
return taxonName;
|
|
384
|
}
|
|
385
|
else{
|
|
386
|
taxonName = TaxonNameFactory.NewBotanicalInstance(null);
|
|
387
|
}
|
|
388
|
taxonName.setFullTitleCache(fullName, true);
|
|
389
|
taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
|
|
390
|
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
|
|
391
|
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
|
|
392
|
try {
|
|
393
|
taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
|
|
394
|
} catch (Exception e) {
|
|
395
|
if (taxonName.getInfraSpecificEpithet() != null){
|
|
396
|
taxonName.setRank(Rank.SUBSPECIES());
|
|
397
|
}
|
|
398
|
else if (taxonName.getSpecificEpithet() != null){
|
|
399
|
taxonName.setRank(Rank.SPECIES());
|
|
400
|
}
|
|
401
|
else if (taxonName.getInfraGenericEpithet() != null){
|
|
402
|
taxonName.setRank(Rank.SUBGENUS());
|
|
403
|
}
|
|
404
|
else if (taxonName.getGenusOrUninomial() != null){
|
|
405
|
taxonName.setRank(Rank.GENUS());
|
|
406
|
}
|
|
407
|
}
|
|
408
|
Team team = null;
|
|
409
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
410
|
team = Team.NewInstance();
|
|
411
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
|
|
412
|
taxonName.setBasionymAuthorship(team);
|
|
413
|
}
|
|
414
|
if (getFromMap(atomisedMap, "AuthorTeam") != null) {
|
|
415
|
team = Team.NewInstance();
|
|
416
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
|
|
417
|
taxonName.setCombinationAuthorship(team);
|
|
418
|
}
|
|
419
|
if (team == null) {
|
|
420
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
421
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
|
|
422
|
}
|
|
423
|
else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
|
|
424
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
|
|
425
|
}
|
|
426
|
}
|
|
427
|
if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
|
|
428
|
team = Team.NewInstance();
|
|
429
|
team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
|
|
430
|
taxonName.setCombinationAuthorship(team);
|
|
431
|
}
|
|
432
|
if (taxonName.hasProblem()) {
|
|
433
|
logger.info("pb ICBN");
|
|
434
|
problem = true;
|
|
435
|
}
|
|
436
|
else {
|
|
437
|
return taxonName;
|
|
438
|
}
|
|
439
|
}
|
|
440
|
else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNB.getUuid())) {
|
|
441
|
TaxonName taxonName = TaxonNameFactory.NewBacterialInstance(null);
|
|
442
|
taxonName.setFullTitleCache(fullName, true);
|
|
443
|
taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
|
|
444
|
taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
|
|
445
|
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
|
|
446
|
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
|
|
447
|
|
|
448
|
if (taxonName.getGenusOrUninomial() != null){
|
|
449
|
taxonName.setRank(Rank.GENUS());
|
|
450
|
}
|
|
451
|
else if (taxonName.getInfraGenericEpithet() != null){
|
|
452
|
taxonName.setRank(Rank.SUBGENUS());
|
|
453
|
}
|
|
454
|
else if (taxonName.getSpecificEpithet() != null){
|
|
455
|
taxonName.setRank(Rank.SPECIES());
|
|
456
|
}
|
|
457
|
else if (taxonName.getInfraSpecificEpithet() != null){
|
|
458
|
taxonName.setRank(Rank.SUBSPECIES());
|
|
459
|
}
|
|
460
|
|
|
461
|
if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
|
|
462
|
Team team = Team.NewInstance();
|
|
463
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
|
|
464
|
taxonName.setCombinationAuthorship(team);
|
|
465
|
}
|
|
466
|
if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
|
|
467
|
Team team = Team.NewInstance();
|
|
468
|
team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
|
|
469
|
taxonName.setBasionymAuthorship(team);
|
|
470
|
}
|
|
471
|
if (taxonName.hasProblem()) {
|
|
472
|
logger.info("pb ICNB");
|
|
473
|
problem = true;
|
|
474
|
}
|
|
475
|
else {
|
|
476
|
return taxonName;
|
|
477
|
}
|
|
478
|
}
|
|
479
|
else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
|
|
480
|
TaxonName taxonName = TaxonNameFactory.NewCultivarInstance(null);
|
|
481
|
|
|
482
|
if (taxonName.hasProblem()) {
|
|
483
|
logger.info("pb ICNCP");
|
|
484
|
problem = true;
|
|
485
|
}
|
|
486
|
else {
|
|
487
|
return taxonName;
|
|
488
|
}
|
|
489
|
return taxonName;
|
|
490
|
}
|
|
491
|
|
|
492
|
if (problem) {
|
|
493
|
logger.info("Problem im setTaxonNameByType ");
|
|
494
|
TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);
|
|
495
|
taxonName.setFullTitleCache(fullName, true);
|
|
496
|
return taxonName;
|
|
497
|
}
|
|
498
|
TaxonName tn = TaxonNameFactory.NewNonViralInstance(null);
|
|
499
|
return tn;
|
|
500
|
}
|
|
501
|
|
|
502
|
/**
|
|
503
|
* Get a formated string from a hashmap
|
|
504
|
* @param atomisedMap
|
|
505
|
* @param key
|
|
506
|
* @return
|
|
507
|
*/
|
|
508
|
private String getFromMap(HashMap<String, String> atomisedMap, String key) {
|
|
509
|
String value = null;
|
|
510
|
if (atomisedMap.containsKey(key)) {
|
|
511
|
value = atomisedMap.get(key);
|
|
512
|
}
|
|
513
|
|
|
514
|
try {
|
|
515
|
if (value != null && key.matches(".*Year.*")) {
|
|
516
|
value = value.trim();
|
|
517
|
if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
|
|
518
|
String tmp = value.split("[0-9]{4}$")[0];
|
|
519
|
int year = Integer.parseInt(value.split(tmp)[1]);
|
|
520
|
if (year >= 1752) {
|
|
521
|
value = tmp;
|
|
522
|
}
|
|
523
|
else {
|
|
524
|
value = null;
|
|
525
|
}
|
|
526
|
}
|
|
527
|
else {
|
|
528
|
value = null;
|
|
529
|
}
|
|
530
|
}
|
|
531
|
}
|
|
532
|
catch (Exception e) {
|
|
533
|
value = null;
|
|
534
|
}
|
|
535
|
return value;
|
|
536
|
}
|
|
537
|
|
|
538
|
/**
|
|
539
|
* Very fast and dirty implementation to allow handling of transient objects as described in
|
|
540
|
* https://dev.e-taxonomy.eu/trac/ticket/3726
|
|
541
|
*
|
|
542
|
* Not yet complete.
|
|
543
|
*
|
|
544
|
* @param cdmBase
|
|
545
|
* @param state
|
|
546
|
*/
|
|
547
|
protected UUID save(CdmBase cdmBase, SpecimenImportStateBase state) {
|
|
548
|
ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
|
|
549
|
if (cdmRepository == null){
|
|
550
|
cdmRepository = this;
|
|
551
|
}
|
|
552
|
|
|
553
|
if (cdmBase.isInstanceOf(LanguageString.class)){
|
|
554
|
return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
|
|
555
|
}else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
|
|
556
|
SpecimenOrObservationBase specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
|
|
557
|
|
|
558
|
return cdmRepository.getOccurrenceService().saveOrUpdate(specimen);
|
|
559
|
}else if (cdmBase.isInstanceOf(Reference.class)){
|
|
560
|
return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
|
|
561
|
}else if (cdmBase.isInstanceOf(Classification.class)){
|
|
562
|
return cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
|
|
563
|
}else if (cdmBase.isInstanceOf(AgentBase.class)){
|
|
564
|
return cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
|
|
565
|
}else if (cdmBase.isInstanceOf(Collection.class)){
|
|
566
|
return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
|
|
567
|
}else if (cdmBase.isInstanceOf(DescriptionBase.class)){
|
|
568
|
DescriptionBase description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
|
|
569
|
|
|
570
|
return cdmRepository.getDescriptionService().saveOrUpdate(description);
|
|
571
|
}else if (cdmBase.isInstanceOf(TaxonBase.class)){
|
|
572
|
return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
|
|
573
|
}else if (cdmBase.isInstanceOf(TaxonName.class)){
|
|
574
|
return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonName.class));
|
|
575
|
}else if (cdmBase.isInstanceOf(TaxonNode.class)){
|
|
576
|
return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.class));
|
|
577
|
}else{
|
|
578
|
throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
|
|
579
|
}
|
|
580
|
|
|
581
|
}
|
|
582
|
|
|
583
|
|
|
584
|
protected SpecimenOrObservationBase findExistingSpecimen(String unitId, SpecimenImportStateBase state){
|
|
585
|
ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
|
|
586
|
if(cdmAppController==null){
|
|
587
|
cdmAppController = this;
|
|
588
|
}
|
|
589
|
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
|
|
590
|
config.setSignificantIdentifier(unitId);
|
|
591
|
Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
|
|
592
|
if(!existingSpecimens.getRecords().isEmpty()){
|
|
593
|
if(existingSpecimens.getRecords().size()==1){
|
|
594
|
return existingSpecimens.getRecords().iterator().next();
|
|
595
|
}
|
|
596
|
}
|
|
597
|
return null;
|
|
598
|
}
|
|
599
|
|
|
600
|
protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
|
|
601
|
|
|
602
|
/**
|
|
603
|
* getFacade : get the DerivedUnitFacade based on the recordBasis
|
|
604
|
* @param state
|
|
605
|
*
|
|
606
|
* @return DerivedUnitFacade
|
|
607
|
*/
|
|
608
|
protected DerivedUnitFacade getFacade(STATE state) {
|
|
609
|
if (logger.isDebugEnabled()){
|
|
610
|
logger.info("getFacade()");
|
|
611
|
}
|
|
612
|
SpecimenOrObservationType type = null;
|
|
613
|
|
|
614
|
// create specimen
|
|
615
|
if (NB((state.getDataHolder().getRecordBasis())) != null) {
|
|
616
|
if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
|
|
617
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
618
|
}
|
|
619
|
if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
|
|
620
|
type = SpecimenOrObservationType.Observation;
|
|
621
|
}
|
|
622
|
if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
|
|
623
|
type = SpecimenOrObservationType.Fossil;
|
|
624
|
}
|
|
625
|
if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
|
|
626
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
627
|
}
|
|
628
|
if (type == null) {
|
|
629
|
logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
|
|
630
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
631
|
}
|
|
632
|
// TODO fossils?
|
|
633
|
} else {
|
|
634
|
logger.info("The basis of record is null");
|
|
635
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
636
|
}
|
|
637
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
638
|
return derivedUnitFacade;
|
|
639
|
}
|
|
640
|
|
|
641
|
/**
|
|
642
|
* Look if the Institution does already exist
|
|
643
|
* @param institutionCode: a string with the institutioncode
|
|
644
|
* @param config : the configurator
|
|
645
|
* @return the Institution (existing or new)
|
|
646
|
*/
|
|
647
|
protected Institution getInstitution(String institutionCode, STATE state) {
|
|
648
|
SpecimenImportConfiguratorBase config = state.getConfig();
|
|
649
|
Institution institution=null;
|
|
650
|
institution = (Institution)state.institutions.get(institutionCode);
|
|
651
|
if (institution != null){
|
|
652
|
return institution;
|
|
653
|
}
|
|
654
|
List<Institution> institutions;
|
|
655
|
try {
|
|
656
|
institutions = getAgentService().searchInstitutionByCode(institutionCode);
|
|
657
|
|
|
658
|
} catch (Exception e) {
|
|
659
|
institutions = new ArrayList<Institution>();
|
|
660
|
logger.warn(e);
|
|
661
|
}
|
|
662
|
if (institutions.size() > 0 && config.isReuseExistingMetaData()) {
|
|
663
|
for (Institution institut:institutions){
|
|
664
|
try{
|
|
665
|
if (institut.getCode().equalsIgnoreCase(institutionCode)) {
|
|
666
|
institution=institut;
|
|
667
|
break;
|
|
668
|
}
|
|
669
|
}catch(Exception e){logger.warn("no institution code in the db");}
|
|
670
|
}
|
|
671
|
}
|
|
672
|
if (logger.isDebugEnabled()){
|
|
673
|
if(institution !=null) {
|
|
674
|
logger.info("getinstitution " + institution.toString());
|
|
675
|
}
|
|
676
|
}
|
|
677
|
if (institution == null){
|
|
678
|
// create institution
|
|
679
|
institution = Institution.NewInstance();
|
|
680
|
institution.setCode(institutionCode);
|
|
681
|
institution.setTitleCache(institutionCode, true);
|
|
682
|
UUID uuid = save(institution, state);
|
|
683
|
}
|
|
684
|
|
|
685
|
|
|
686
|
state.institutions.put(institutionCode, institution);
|
|
687
|
return institution;
|
|
688
|
}
|
|
689
|
|
|
690
|
/**
|
|
691
|
* Look if the Collection does already exist
|
|
692
|
* @param collectionCode
|
|
693
|
* @param collectionCode: a string
|
|
694
|
* @param config : the configurator
|
|
695
|
* @return the Collection (existing or new)
|
|
696
|
*/
|
|
697
|
protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
|
|
698
|
SpecimenImportConfiguratorBase config = state.getConfig();
|
|
699
|
Collection collection = null;
|
|
700
|
List<Collection> collections;
|
|
701
|
collection = (Collection) state.collections.get(collectionCode);
|
|
702
|
if (collection != null){
|
|
703
|
return collection;
|
|
704
|
}
|
|
705
|
try {
|
|
706
|
collections = getCollectionService().searchByCode(collectionCode);
|
|
707
|
} catch (Exception e) {
|
|
708
|
collections = new ArrayList<Collection>();
|
|
709
|
}
|
|
710
|
if (collections.size() > 0 && config.isReuseExistingMetaData()) {
|
|
711
|
for (Collection coll:collections){
|
|
712
|
if (coll.getCode() != null && coll.getInstitute() != null
|
|
713
|
&& coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
|
|
714
|
collection = coll;
|
|
715
|
break;
|
|
716
|
}
|
|
717
|
}
|
|
718
|
}
|
|
719
|
|
|
720
|
if(collection == null){
|
|
721
|
collection =Collection.NewInstance();
|
|
722
|
collection.setCode(collectionCode);
|
|
723
|
collection.setInstitute(institution);
|
|
724
|
collection.setTitleCache(collectionCode);
|
|
725
|
UUID uuid = save(collection, state);
|
|
726
|
}
|
|
727
|
|
|
728
|
|
|
729
|
|
|
730
|
state.collections.put(collectionCode, collection);
|
|
731
|
|
|
732
|
return collection;
|
|
733
|
}
|
|
734
|
|
|
735
|
/**
|
|
736
|
* @param reference
|
|
737
|
* @param citationDetail
|
|
738
|
* @return
|
|
739
|
*/
|
|
740
|
//FIXME this method is highly critical, because
|
|
741
|
// * it will have serious performance and memory problems with large databases
|
|
742
|
// (databases may easily have >1 Mio source records)
|
|
743
|
// * it does not make sense to search for existing sources and then clone them
|
|
744
|
// we need to search for existing references instead and use them (if exist)
|
|
745
|
// for our new source.
|
|
746
|
protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
|
|
747
|
|
|
748
|
/* List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
749
|
|
|
750
|
|
|
751
|
if (reference != null){
|
|
752
|
try {
|
|
753
|
for (OriginalSourceBase<?> osb: issTmp){
|
|
754
|
if (osb.getCitation() != null && osb.getCitation().getTitleCache().equalsIgnoreCase(reference.getTitleCache())){
|
|
755
|
String osbDetail = osb.getCitationMicroReference();
|
|
756
|
if ((StringUtils.isBlank(osbDetail) && StringUtils.isBlank(citationDetail))
|
|
757
|
|| (osbDetail != null && osbDetail.equalsIgnoreCase(citationDetail)) ) {
|
|
758
|
// System.out.println("REFERENCE FOUND RETURN EXISTING SOURCE");
|
|
759
|
return (IdentifiableSource) osb.clone();
|
|
760
|
}
|
|
761
|
}
|
|
762
|
}
|
|
763
|
} catch (CloneNotSupportedException e) {
|
|
764
|
throw new RuntimeException(e);
|
|
765
|
} catch (Exception e1){
|
|
766
|
e1.printStackTrace();
|
|
767
|
}
|
|
768
|
}
|
|
769
|
*/
|
|
770
|
IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
|
|
771
|
return sour;
|
|
772
|
}
|
|
773
|
|
|
774
|
/**
|
|
775
|
* Add the hierarchy for a Taxon(add higher taxa)
|
|
776
|
* @param classification
|
|
777
|
* @param taxon: a taxon to add as a node
|
|
778
|
* @param state: the ABCD import state
|
|
779
|
*/
|
|
780
|
protected void addParentTaxon(Taxon taxon, STATE state, boolean preferredFlag, Classification classification){
|
|
781
|
INonViralName nvname = taxon.getName();
|
|
782
|
Rank rank = nvname.getRank();
|
|
783
|
Taxon genus =null;
|
|
784
|
Taxon subgenus =null;
|
|
785
|
Taxon species = null;
|
|
786
|
Taxon subspecies = null;
|
|
787
|
Taxon parent = null;
|
|
788
|
if(rank!=null){
|
|
789
|
if (rank.isLower(Rank.GENUS() )){
|
|
790
|
String genusOrUninomial = nvname.getGenusOrUninomial();
|
|
791
|
TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
|
|
792
|
genus = getOrCreateTaxonForName(taxonName, state);
|
|
793
|
if (genus == null){
|
|
794
|
logger.debug("The genus should not be null " + taxonName);
|
|
795
|
}
|
|
796
|
if (preferredFlag) {
|
|
797
|
parent = linkParentChildNode(null, genus, classification, state);
|
|
798
|
}
|
|
799
|
|
|
800
|
}
|
|
801
|
if (rank.isLower(Rank.SUBGENUS())){
|
|
802
|
String prefix = nvname.getGenusOrUninomial();
|
|
803
|
String name = nvname.getInfraGenericEpithet();
|
|
804
|
if (name != null){
|
|
805
|
TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
|
|
806
|
subgenus = getOrCreateTaxonForName(taxonName, state);
|
|
807
|
if (preferredFlag) {
|
|
808
|
parent = linkParentChildNode(genus, subgenus, classification, state);
|
|
809
|
} }
|
|
810
|
}
|
|
811
|
if (rank.isLower(Rank.SPECIES())){
|
|
812
|
if (subgenus!=null){
|
|
813
|
String prefix = nvname.getGenusOrUninomial();
|
|
814
|
String name = nvname.getInfraGenericEpithet();
|
|
815
|
String spe = nvname.getSpecificEpithet();
|
|
816
|
if (spe != null){
|
|
817
|
TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
|
|
818
|
species = getOrCreateTaxonForName(taxonName, state);
|
|
819
|
if (preferredFlag) {
|
|
820
|
parent = linkParentChildNode(subgenus, species, classification, state);
|
|
821
|
}
|
|
822
|
}
|
|
823
|
}
|
|
824
|
else{
|
|
825
|
String prefix = nvname.getGenusOrUninomial();
|
|
826
|
String name = nvname.getSpecificEpithet();
|
|
827
|
if (name != null){
|
|
828
|
TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
|
|
829
|
species = getOrCreateTaxonForName(taxonName, state);
|
|
830
|
if (preferredFlag) {
|
|
831
|
parent = linkParentChildNode(genus, species, classification, state);
|
|
832
|
}
|
|
833
|
}
|
|
834
|
}
|
|
835
|
}
|
|
836
|
if (rank.isLower(Rank.INFRASPECIES())){
|
|
837
|
TaxonName taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
|
|
838
|
subspecies = getOrCreateTaxonForName(taxonName, state);
|
|
839
|
if (preferredFlag) {
|
|
840
|
parent = linkParentChildNode(species, subspecies, classification, state);
|
|
841
|
}
|
|
842
|
}
|
|
843
|
}
|
|
844
|
if (preferredFlag && parent!=taxon ) {
|
|
845
|
linkParentChildNode(parent, taxon, classification, state);
|
|
846
|
}
|
|
847
|
}
|
|
848
|
|
|
849
|
/**
|
|
850
|
* Link a parent to a child and save it in the current classification
|
|
851
|
* @param parent: the higher Taxon
|
|
852
|
* @param child : the lower (or current) Taxon
|
|
853
|
* return the Taxon from the new created Node
|
|
854
|
* @param classification
|
|
855
|
* @param state
|
|
856
|
*/
|
|
857
|
protected Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, STATE state) {
|
|
858
|
TaxonNode node =null;
|
|
859
|
if (parent != null) {
|
|
860
|
parent = (Taxon) getTaxonService().find(parent.getUuid());
|
|
861
|
child = (Taxon) getTaxonService().find(child.getUuid());
|
|
862
|
//here we do not have to check if the taxon nodes already exists
|
|
863
|
//this is done by classification.addParentChild()
|
|
864
|
//do not add child node if it already exists
|
|
865
|
if(hasTaxonNodeInClassification(child, classification)){
|
|
866
|
return child;
|
|
867
|
}
|
|
868
|
else{
|
|
869
|
node = classification.addParentChild(parent, child, state.getRef(), "");
|
|
870
|
save(node, state);
|
|
871
|
}
|
|
872
|
}
|
|
873
|
else {
|
|
874
|
if (child == null){
|
|
875
|
logger.debug("The child should not be null!");
|
|
876
|
}
|
|
877
|
child = (Taxon) getTaxonService().find(child.getUuid());
|
|
878
|
//do not add child node if it already exists
|
|
879
|
if(hasTaxonNodeInClassification(child, classification)){
|
|
880
|
return child;
|
|
881
|
}
|
|
882
|
else{
|
|
883
|
node = classification.addChildTaxon(child, state.getRef(), null);
|
|
884
|
save(node, state);
|
|
885
|
}
|
|
886
|
}
|
|
887
|
if(node!=null){
|
|
888
|
state.getReport().addTaxonNode(node);
|
|
889
|
return node.getTaxon();
|
|
890
|
}
|
|
891
|
String message = "Could not create taxon node for " +child;
|
|
892
|
state.getReport().addInfoMessage(message);
|
|
893
|
logger.warn(message);
|
|
894
|
return null;
|
|
895
|
}
|
|
896
|
|
|
897
|
protected Taxon getOrCreateTaxonForName(TaxonName taxonName, STATE state){
|
|
898
|
if (taxonName != null){
|
|
899
|
Set<Taxon> acceptedTaxa = taxonName.getTaxa();
|
|
900
|
if(acceptedTaxa.size()>0){
|
|
901
|
Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
|
|
902
|
if(acceptedTaxa.size()>1){
|
|
903
|
String message = "More than one accepted taxon was found for taxon name: "
|
|
904
|
+ taxonName.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
|
|
905
|
state.getReport().addInfoMessage(message);
|
|
906
|
logger.warn(message);
|
|
907
|
}
|
|
908
|
else{
|
|
909
|
return firstAcceptedTaxon;
|
|
910
|
}
|
|
911
|
}
|
|
912
|
else{
|
|
913
|
Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases();
|
|
914
|
for (TaxonBase taxonBase : taxonAndSynonyms) {
|
|
915
|
if(taxonBase.isInstanceOf(Synonym.class)){
|
|
916
|
Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
|
|
917
|
Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon();
|
|
918
|
if(acceptedTaxonOfSynonym == null){
|
|
919
|
String message = "No accepted taxon could be found for taxon name: "
|
|
920
|
+ taxonName.getTitleCache()
|
|
921
|
+ "!";
|
|
922
|
state.getReport().addInfoMessage(message);
|
|
923
|
logger.warn(message);
|
|
924
|
}
|
|
925
|
else{
|
|
926
|
return acceptedTaxonOfSynonym;
|
|
927
|
}
|
|
928
|
}
|
|
929
|
}
|
|
930
|
}
|
|
931
|
Taxon taxon = Taxon.NewInstance(taxonName, state.getRef());
|
|
932
|
save(taxon, state);
|
|
933
|
state.getReport().addTaxon(taxon);
|
|
934
|
logger.info("Created new taxon "+ taxon);
|
|
935
|
return taxon;
|
|
936
|
}
|
|
937
|
return null;
|
|
938
|
|
|
939
|
}
|
|
940
|
|
|
941
|
private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
|
|
942
|
if(taxon.getTaxonNodes()!=null){
|
|
943
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
944
|
if(node.getClassification().equals(classification)){
|
|
945
|
return true;
|
|
946
|
}
|
|
947
|
}
|
|
948
|
}
|
|
949
|
return false;
|
|
950
|
}
|
|
951
|
|
|
952
|
/**
|
|
953
|
* HandleIdentifications : get the scientific names present in the ABCD
|
|
954
|
* document and store link them with the observation/specimen data
|
|
955
|
* @param state: the current ABCD import state
|
|
956
|
* @param derivedUnitFacade : the current derivedunitfacade
|
|
957
|
*/
|
|
958
|
protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
|
|
959
|
SpecimenImportConfiguratorBase config = state.getConfig();
|
|
960
|
|
|
961
|
|
|
962
|
String scientificName = "";
|
|
963
|
boolean preferredFlag = false;
|
|
964
|
|
|
965
|
if (state.getDataHolder().getNomenclatureCode() == ""){
|
|
966
|
if (config.getNomenclaturalCode() != null){
|
|
967
|
if (config.getNomenclaturalCode() != null){
|
|
968
|
state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
|
|
969
|
|
|
970
|
}
|
|
971
|
}
|
|
972
|
}
|
|
973
|
|
|
974
|
for (int i = 0; i < state.getDataHolder().getIdentificationList().size(); i++) {
|
|
975
|
Identification identification = state.getDataHolder().getIdentificationList().get(i);
|
|
976
|
scientificName = identification.getScientificName().replaceAll(" et ", " & ");
|
|
977
|
|
|
978
|
String preferred = identification.getPreferred();
|
|
979
|
preferredFlag = false;
|
|
980
|
if (preferred != null){
|
|
981
|
if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || state.getDataHolder().getIdentificationList().size()==1) {
|
|
982
|
preferredFlag = true;
|
|
983
|
}
|
|
984
|
|
|
985
|
}
|
|
986
|
if (identification.getCode() != null){
|
|
987
|
if (identification.getCode().indexOf(':') != -1) {
|
|
988
|
state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
|
|
989
|
}
|
|
990
|
else{
|
|
991
|
state.getDataHolder().setNomenclatureCode(identification.getCode());
|
|
992
|
}
|
|
993
|
}
|
|
994
|
TaxonName taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
|
|
995
|
Taxon taxon = getOrCreateTaxonForName(taxonName, state);
|
|
996
|
addTaxonNode(taxon, state,preferredFlag);
|
|
997
|
linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate());
|
|
998
|
}
|
|
999
|
}
|
|
1000
|
|
|
1001
|
/**
|
|
1002
|
* @param taxon : a taxon to add as a node
|
|
1003
|
* @param state : the ABCD import state
|
|
1004
|
*/
|
|
1005
|
protected void addTaxonNode(Taxon taxon, STATE state, boolean preferredFlag) {
|
|
1006
|
SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
|
|
1007
|
logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
|
|
1008
|
//only add nodes if not already existing in current classification or default classification
|
|
1009
|
|
|
1010
|
//check if node exists in current classification
|
|
1011
|
//NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
|
|
1012
|
if (!existsInClassification(taxon,state.getClassification(), state)){
|
|
1013
|
if(config.isMoveNewTaxaToDefaultClassification()){
|
|
1014
|
//check if node exists in default classification
|
|
1015
|
if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
|
|
1016
|
addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
|
|
1017
|
}
|
|
1018
|
}else{
|
|
1019
|
//add non-existing taxon to current classification
|
|
1020
|
addParentTaxon(taxon, state, preferredFlag, state.getClassification());
|
|
1021
|
}
|
|
1022
|
|
|
1023
|
}
|
|
1024
|
}
|
|
1025
|
|
|
1026
|
|
|
1027
|
private boolean existsInClassification(Taxon taxon, Classification classification, STATE state){
|
|
1028
|
boolean exist = false;
|
|
1029
|
ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
|
|
1030
|
if(cdmAppController==null){
|
|
1031
|
cdmAppController = this;
|
|
1032
|
}
|
|
1033
|
if (classification != null){
|
|
1034
|
if (!taxon.getTaxonNodes().isEmpty()){
|
|
1035
|
for (TaxonNode node:taxon.getTaxonNodes()){
|
|
1036
|
if (node.getClassification().equals(classification)){
|
|
1037
|
return true;
|
|
1038
|
}
|
|
1039
|
}
|
|
1040
|
}
|
|
1041
|
// we do not need this because we already searched for taxa in db in the previous steps
|
|
1042
|
// List<UuidAndTitleCache<TaxonNode>> uuidAndTitleCacheOfAllTaxa = cdmAppController.getClassificationService().getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification.getUuid());
|
|
1043
|
// if (uuidAndTitleCacheOfAllTaxa != null){
|
|
1044
|
// for (UuidAndTitleCache p : uuidAndTitleCacheOfAllTaxa){
|
|
1045
|
// try{
|
|
1046
|
// if(p.getTitleCache().equals(taxon.getTitleCache())) {
|
|
1047
|
// exist = true;
|
|
1048
|
// }
|
|
1049
|
// }
|
|
1050
|
// catch(Exception e){
|
|
1051
|
// logger.warn("TaxonNode doesn't seem to have a taxon");
|
|
1052
|
// }
|
|
1053
|
// }
|
|
1054
|
// }
|
|
1055
|
}
|
|
1056
|
return exist;
|
|
1057
|
}
|
|
1058
|
|
|
1059
|
/**
|
|
1060
|
* join DeterminationEvent to the Taxon Object
|
|
1061
|
* @param state : the ABCD import state
|
|
1062
|
* @param taxon: the current Taxon
|
|
1063
|
* @param preferredFlag :if the current name is preferred
|
|
1064
|
* @param derivedFacade : the derived Unit Facade
|
|
1065
|
*/
|
|
1066
|
@SuppressWarnings("rawtypes")
|
|
1067
|
protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade, String identifierStr, String dateStr) {
|
|
1068
|
SpecimenImportConfiguratorBase config = state.getConfig();
|
|
1069
|
if (logger.isDebugEnabled()){
|
|
1070
|
logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
|
|
1071
|
}
|
|
1072
|
|
|
1073
|
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
|
|
1074
|
determinationEvent.setTaxonName(taxon.getName());
|
|
1075
|
determinationEvent.setPreferredFlag(preferredFlag);
|
|
1076
|
|
|
1077
|
|
|
1078
|
determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
|
|
1079
|
if (state.getPersonStore().get(identifierStr) != null){
|
|
1080
|
determinationEvent.setActor((AgentBase)state.getPersonStore().get(identifierStr));
|
|
1081
|
} else if (identifierStr != null){
|
|
1082
|
Person identifier = Person.NewTitledInstance(identifierStr);
|
|
1083
|
determinationEvent.setActor(identifier);
|
|
1084
|
}
|
|
1085
|
if (dateStr != null){
|
|
1086
|
determinationEvent.setTimeperiod(TimePeriodParser.parseString(dateStr));
|
|
1087
|
}
|
|
1088
|
state.getDerivedUnitBase().addDetermination(determinationEvent);
|
|
1089
|
|
|
1090
|
if (logger.isDebugEnabled()){
|
|
1091
|
logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
|
|
1092
|
}
|
|
1093
|
for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().getStatusList()) {
|
|
1094
|
if (specimenTypeDesignationstatus != null) {
|
|
1095
|
if (logger.isDebugEnabled()){
|
|
1096
|
logger.debug("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
|
|
1097
|
}
|
|
1098
|
|
|
1099
|
ICdmRepository cdmAppController = config.getCdmAppController();
|
|
1100
|
if(cdmAppController == null){
|
|
1101
|
cdmAppController = this;
|
|
1102
|
}
|
|
1103
|
specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid());
|
|
1104
|
//Designation
|
|
1105
|
TaxonName name = taxon.getName();
|
|
1106
|
SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
|
|
1107
|
|
|
1108
|
designation.setTypeStatus(specimenTypeDesignationstatus);
|
|
1109
|
designation.setTypeSpecimen(state.getDerivedUnitBase());
|
|
1110
|
name.addTypeDesignation(designation, true);
|
|
1111
|
}
|
|
1112
|
}
|
|
1113
|
|
|
1114
|
for (String[] fullReference : state.getDataHolder().getReferenceList()) {
|
|
1115
|
|
|
1116
|
|
|
1117
|
String strReference=fullReference[0];
|
|
1118
|
String citationDetail = fullReference[1];
|
|
1119
|
String citationURL = fullReference[2];
|
|
1120
|
List<Reference> references = getReferenceService().listByTitle(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
|
|
1121
|
|
|
1122
|
if (!references.isEmpty()){
|
|
1123
|
Reference reference = null;
|
|
1124
|
for (Reference refe: references) {
|
|
1125
|
if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
|
|
1126
|
reference =refe;
|
|
1127
|
break;
|
|
1128
|
}
|
|
1129
|
}
|
|
1130
|
if (reference ==null){
|
|
1131
|
reference = ReferenceFactory.newGeneric();
|
|
1132
|
reference.setTitleCache(strReference, true);
|
|
1133
|
save(reference, state);
|
|
1134
|
}
|
|
1135
|
determinationEvent.addReference(reference);
|
|
1136
|
}
|
|
1137
|
}
|
|
1138
|
save(state.getDerivedUnitBase(), state);
|
|
1139
|
|
|
1140
|
if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
|
|
1141
|
//do not add IndividualsAssociation to non-preferred taxa
|
|
1142
|
if (logger.isDebugEnabled()){
|
|
1143
|
logger.debug("isDoCreateIndividualsAssociations");
|
|
1144
|
}
|
|
1145
|
|
|
1146
|
makeIndividualsAssociation(state, taxon, determinationEvent);
|
|
1147
|
|
|
1148
|
save(state.getDerivedUnitBase(), state);
|
|
1149
|
}
|
|
1150
|
}
|
|
1151
|
|
|
1152
|
/**
|
|
1153
|
* create and link each association (specimen, observation..) to the accepted taxon
|
|
1154
|
* @param state : the ABCD import state
|
|
1155
|
* @param taxon: the current Taxon
|
|
1156
|
* @param determinationEvent:the determinationevent
|
|
1157
|
*/
|
|
1158
|
protected void makeIndividualsAssociation(STATE state, Taxon taxon, DeterminationEvent determinationEvent) {
|
|
1159
|
SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
|
|
1160
|
SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
|
|
1161
|
|
|
1162
|
if (logger.isDebugEnabled()){
|
|
1163
|
logger.info("MAKE INDIVIDUALS ASSOCIATION");
|
|
1164
|
}
|
|
1165
|
|
|
1166
|
TaxonDescription taxonDescription = null;
|
|
1167
|
Set<TaxonDescription> descriptions= taxon.getDescriptions();
|
|
1168
|
if (!descriptions.isEmpty()){ taxonDescription = descriptions.iterator().next();}
|
|
1169
|
|
|
1170
|
// for (TaxonDescription description : descriptions){
|
|
1171
|
// Set<IdentifiableSource> sources = new HashSet<>();
|
|
1172
|
// sources.addAll(description.getTaxon().getSources());
|
|
1173
|
// sources.addAll(description.getSources());
|
|
1174
|
// for (IdentifiableSource source:sources){
|
|
1175
|
// if(state.getRef().equals(source.getCitation())) {
|
|
1176
|
// taxonDescription = description;
|
|
1177
|
// }
|
|
1178
|
// }
|
|
1179
|
// }
|
|
1180
|
// }
|
|
1181
|
if (taxonDescription == null){
|
|
1182
|
taxonDescription = TaxonDescription.NewInstance(taxon, false);
|
|
1183
|
if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
|
|
1184
|
taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
|
|
1185
|
}
|
|
1186
|
state.setDescriptionGroup(taxonDescription);
|
|
1187
|
taxon.addDescription(taxonDescription);
|
|
1188
|
}
|
|
1189
|
|
|
1190
|
//PREPARE REFERENCE QUESTIONS
|
|
1191
|
|
|
1192
|
Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
|
|
1193
|
|
|
1194
|
List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
1195
|
List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
1196
|
|
|
1197
|
Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
|
|
1198
|
if(issTmp2!=null) {
|
|
1199
|
osbSet.addAll(issTmp2);
|
|
1200
|
}
|
|
1201
|
if(issTmp!=null) {
|
|
1202
|
osbSet.addAll(issTmp);
|
|
1203
|
}
|
|
1204
|
|
|
1205
|
|
|
1206
|
addToSourceMap(sourceMap, osbSet);
|
|
1207
|
|
|
1208
|
// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
|
|
1209
|
// List<OriginalSourceBase<?>> res = null;
|
|
1210
|
// if(!state.isDescriptionSourcesSet()){
|
|
1211
|
// res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
|
|
1212
|
// "The current reference is "+state.getRef().getTitleCache(),getReferenceService(), state.getDataHolder().docSources);
|
|
1213
|
// state.setDescriptionRefs(res);
|
|
1214
|
// state.setDescriptionSourcesSet(true);
|
|
1215
|
// }
|
|
1216
|
// else{
|
|
1217
|
// res=state.getDescriptionRefs();
|
|
1218
|
// }
|
|
1219
|
// if(res !=null) {
|
|
1220
|
// for (OriginalSourceBase<?> sour:res){
|
|
1221
|
// if(sour.isInstanceOf(IdentifiableSource.class)){
|
|
1222
|
// try {
|
|
1223
|
// if(sourceNotLinkedToElement(taxonDescription,sour)) {
|
|
1224
|
// taxonDescription.addSource((IdentifiableSource)sour.clone());
|
|
1225
|
// }
|
|
1226
|
// } catch (CloneNotSupportedException e) {
|
|
1227
|
// logger.warn("no cloning?");
|
|
1228
|
// }
|
|
1229
|
// }else{
|
|
1230
|
// if(sourceNotLinkedToElement(taxonDescription,sour)) {
|
|
1231
|
// taxonDescription.addSource(OriginalSourceType.Import,null, null, sour.getCitation(),sour.getCitationMicroReference());
|
|
1232
|
// }
|
|
1233
|
// }
|
|
1234
|
// }
|
|
1235
|
// }
|
|
1236
|
// }
|
|
1237
|
// else {
|
|
1238
|
if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
|
|
1239
|
taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1240
|
}
|
|
1241
|
// }
|
|
1242
|
state.setDescriptionGroup(taxonDescription);
|
|
1243
|
|
|
1244
|
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
|
|
1245
|
Feature feature = makeFeature(state.getDerivedUnitBase());
|
|
1246
|
indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
|
|
1247
|
indAssociation.setFeature(feature);
|
|
1248
|
//
|
|
1249
|
// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
|
|
1250
|
// sourceMap = new HashMap<String, OriginalSourceBase<?>>();
|
|
1251
|
//
|
|
1252
|
// issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
1253
|
// issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
1254
|
//
|
|
1255
|
// osbSet = new HashSet<OriginalSourceBase>();
|
|
1256
|
// if(issTmp2!=null) {
|
|
1257
|
// osbSet.addAll(issTmp2);
|
|
1258
|
// }
|
|
1259
|
// if(issTmp!=null) {
|
|
1260
|
// osbSet.addAll(issTmp);
|
|
1261
|
// }
|
|
1262
|
//
|
|
1263
|
//
|
|
1264
|
// addToSourceMap(sourceMap, osbSet);
|
|
1265
|
//
|
|
1266
|
// List<OriginalSourceBase<?>> sources =null;
|
|
1267
|
// if(!state.isAssociationSourcesSet()) {
|
|
1268
|
// sources = sui.askForSource(sourceMap, "descriptive element (association) ",taxon.toString(),
|
|
1269
|
// getReferenceService(),state.getDataHolder().getDocSources());
|
|
1270
|
// state.setAssociationRefs(sources);
|
|
1271
|
// state.setAssociationSourcesSet(true);
|
|
1272
|
// }
|
|
1273
|
// else{
|
|
1274
|
// sources=state.getAssociationRefs();
|
|
1275
|
// }
|
|
1276
|
// if(sources !=null) {
|
|
1277
|
// for (OriginalSourceBase<?> source: sources) {
|
|
1278
|
// if(source !=null) {
|
|
1279
|
// if(source.isInstanceOf(DescriptionElementSource.class)){
|
|
1280
|
// try {
|
|
1281
|
// if(sourceNotLinkedToElement(indAssociation,source)) {
|
|
1282
|
// indAssociation.addSource((DescriptionElementSource)source.clone());
|
|
1283
|
// }
|
|
1284
|
// } catch (CloneNotSupportedException e) {
|
|
1285
|
// logger.warn("clone forbidden?");
|
|
1286
|
// }
|
|
1287
|
// }else{
|
|
1288
|
// if(sourceNotLinkedToElement(indAssociation,source)) {
|
|
1289
|
// indAssociation.addSource(OriginalSourceType.Import,null, null, source.getCitation(),source.getCitationMicroReference());
|
|
1290
|
// }
|
|
1291
|
// try {
|
|
1292
|
// if(sourceNotLinkedToElement(state.getDerivedUnitBase(), source)) {
|
|
1293
|
// state.getDerivedUnitBase().addSource((IdentifiableSource) source.clone());
|
|
1294
|
// }
|
|
1295
|
// } catch (CloneNotSupportedException e) {
|
|
1296
|
// // TODO Auto-generated catch block
|
|
1297
|
// e.printStackTrace();
|
|
1298
|
// }
|
|
1299
|
// }
|
|
1300
|
//
|
|
1301
|
// }
|
|
1302
|
// }
|
|
1303
|
// }
|
|
1304
|
// }else {
|
|
1305
|
if(sourceNotLinkedToElement(indAssociation,state.getRef(),null)) {
|
|
1306
|
indAssociation.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1307
|
}
|
|
1308
|
if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
|
|
1309
|
state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1310
|
}
|
|
1311
|
for (Reference citation : determinationEvent.getReferences()) {
|
|
1312
|
if(sourceNotLinkedToElement(indAssociation,citation,null))
|
|
1313
|
{
|
|
1314
|
indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
|
|
1315
|
}
|
|
1316
|
if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
|
|
1317
|
state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1318
|
}
|
|
1319
|
}
|
|
1320
|
// }
|
|
1321
|
|
|
1322
|
taxonDescription.addElement(indAssociation);
|
|
1323
|
|
|
1324
|
save(taxonDescription, state);
|
|
1325
|
save(taxon, state);
|
|
1326
|
state.getReport().addDerivate(state.getDerivedUnitBase(), config);
|
|
1327
|
state.getReport().addIndividualAssociation(taxon, state.getDataHolder().getUnitID(), state.getDerivedUnitBase());
|
|
1328
|
}
|
|
1329
|
|
|
1330
|
/**
|
|
1331
|
* @param derivedUnitBase2
|
|
1332
|
* @param ref2
|
|
1333
|
* @param object
|
|
1334
|
* @return
|
|
1335
|
*/
|
|
1336
|
private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference b, String d) {
|
|
1337
|
Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
|
|
1338
|
for (IdentifiableSource is:linkedSources){
|
|
1339
|
Reference a = is.getCitation();
|
|
1340
|
String c = is.getCitationMicroReference();
|
|
1341
|
|
|
1342
|
boolean refMatch=false;
|
|
1343
|
boolean microMatch=false;
|
|
1344
|
|
|
1345
|
try{
|
|
1346
|
if (a==null && b==null) {
|
|
1347
|
refMatch=true;
|
|
1348
|
}
|
|
1349
|
if (a!=null && b!=null) {
|
|
1350
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1351
|
refMatch=true;
|
|
1352
|
}
|
|
1353
|
}
|
|
1354
|
}catch(Exception e){}
|
|
1355
|
|
|
1356
|
|
|
1357
|
try{
|
|
1358
|
if (c==null && d==null) {
|
|
1359
|
microMatch=true;
|
|
1360
|
}
|
|
1361
|
if(c!=null && d!=null) {
|
|
1362
|
if(c.equalsIgnoreCase(d)) {
|
|
1363
|
microMatch=true;
|
|
1364
|
}
|
|
1365
|
}
|
|
1366
|
}
|
|
1367
|
catch(Exception e){}
|
|
1368
|
|
|
1369
|
if (microMatch && refMatch) {
|
|
1370
|
return false;
|
|
1371
|
}
|
|
1372
|
|
|
1373
|
|
|
1374
|
}
|
|
1375
|
return true;
|
|
1376
|
}
|
|
1377
|
|
|
1378
|
private <T extends OriginalSourceBase<?>> boolean sourceNotLinkedToElement(ISourceable<T> sourcable, Reference reference, String microReference) {
|
|
1379
|
Set<T> linkedSources = sourcable.getSources();
|
|
1380
|
for (T is:linkedSources){
|
|
1381
|
Reference unitReference = is.getCitation();
|
|
1382
|
String unitMicroReference = is.getCitationMicroReference();
|
|
1383
|
|
|
1384
|
boolean refMatch=false;
|
|
1385
|
boolean microMatch=false;
|
|
1386
|
|
|
1387
|
try{
|
|
1388
|
if (unitReference==null && reference==null) {
|
|
1389
|
refMatch=true;
|
|
1390
|
}
|
|
1391
|
if (unitReference!=null && reference!=null) {
|
|
1392
|
if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
|
|
1393
|
refMatch=true;
|
|
1394
|
}
|
|
1395
|
}
|
|
1396
|
}catch(Exception e){}
|
|
1397
|
|
|
1398
|
try{
|
|
1399
|
if (unitMicroReference==null && microReference==null) {
|
|
1400
|
microMatch=true;
|
|
1401
|
}
|
|
1402
|
if(unitMicroReference!=null && microReference!=null) {
|
|
1403
|
if(unitMicroReference.equalsIgnoreCase(microReference)) {
|
|
1404
|
microMatch=true;
|
|
1405
|
}
|
|
1406
|
}
|
|
1407
|
}
|
|
1408
|
catch(Exception e){}
|
|
1409
|
|
|
1410
|
if (microMatch && refMatch) {
|
|
1411
|
return false;
|
|
1412
|
}
|
|
1413
|
}
|
|
1414
|
return true;
|
|
1415
|
}
|
|
1416
|
|
|
1417
|
/**
|
|
1418
|
* look for the Feature object (FieldObs, Specimen,...)
|
|
1419
|
* @param unit : a specimen or obersvation base
|
|
1420
|
* @return the corresponding Feature
|
|
1421
|
*/
|
|
1422
|
private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
|
|
1423
|
SpecimenOrObservationType type = unit.getRecordBasis();
|
|
1424
|
|
|
1425
|
|
|
1426
|
|
|
1427
|
if (type.isFeatureObservation()){
|
|
1428
|
return Feature.OBSERVATION();
|
|
1429
|
}else if (type.isFeatureSpecimen()){
|
|
1430
|
return Feature.SPECIMEN();
|
|
1431
|
}else if (type == SpecimenOrObservationType.DerivedUnit){
|
|
1432
|
return Feature.OBSERVATION();
|
|
1433
|
// return getFeature("Specimen or observation");
|
|
1434
|
}else{
|
|
1435
|
String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
|
|
1436
|
logger.warn(String.format(message, type.getMessage()));
|
|
1437
|
return Feature.OBSERVATION();
|
|
1438
|
// return getFeature("Specimen or observation");
|
|
1439
|
|
|
1440
|
}
|
|
1441
|
}
|
|
1442
|
|
|
1443
|
|
|
1444
|
/**
|
|
1445
|
* @param sourceMap
|
|
1446
|
* @param osbSet
|
|
1447
|
*/
|
|
1448
|
protected void addToSourceMap(Map<String, OriginalSourceBase<?>> sourceMap, Set<OriginalSourceBase> osbSet) {
|
|
1449
|
for( OriginalSourceBase<?> osb:osbSet) {
|
|
1450
|
if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
|
|
1451
|
try{
|
|
1452
|
sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
|
|
1453
|
}catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
|
|
1454
|
} else if(osb.getCitation()!=null){
|
|
1455
|
try{
|
|
1456
|
sourceMap.put(osb.getCitation().getTitleCache(),osb);
|
|
1457
|
}catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
|
|
1458
|
}
|
|
1459
|
}
|
|
1460
|
}
|
|
1461
|
|
|
1462
|
|
|
1463
|
}
|