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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.taxonx;
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import java.util.ArrayList;
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import java.util.HashMap;
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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 org.apache.log4j.Logger;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.ICommonService;
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import eu.etaxonomy.cdm.api.service.INameService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.CdmIoBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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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/**
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* @author a.mueller
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* @created 29.07.2008
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* @version 1.0
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*/
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@Component
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public class TaxonXNomenclatureImport extends CdmIoBase<TaxonXImportState> implements ICdmIO<TaxonXImportState> {
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private static final Logger logger = Logger.getLogger(TaxonXNomenclatureImport.class);
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@SuppressWarnings("unused")
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private static int modCount = 10000;
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public TaxonXNomenclatureImport(){
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super();
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}
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@Override
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public boolean doCheck(TaxonXImportState state){
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boolean result = true;
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logger.warn("Checking for Types not yet implemented");
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//result &= checkArticlesWithoutJournal(bmiConfig);
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//result &= checkPartOfJournal(bmiConfig);
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return result;
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}
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@Override
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public void doInvoke(TaxonXImportState state){
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logger.info("start make Nomenclature ...");
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TransactionStatus tx = startTransaction();
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TaxonXImportConfigurator config = state.getConfig();
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Element root = config.getSourceRoot();
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Namespace nsTaxonx = root.getNamespace();
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//for testing only
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Taxon taxon = getTaxon(config);
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boolean isChanged = false;
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Element elTaxonBody = root.getChild("taxonxBody", nsTaxonx);
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Element elTreatment = elTaxonBody.getChild("treatment", nsTaxonx);
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Element elNomenclature = elTreatment.getChild("nomenclature", nsTaxonx);
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//isChanged |= doCollectionEvent(txConfig, elNomenclature, nsTaxonx, taxon);
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if (taxon != null && taxon.getName() != null && elNomenclature != null){
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isChanged |= doNomenclaturalType(config, elNomenclature, nsTaxonx, taxon.getName());
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List<Element> elSynonymyList = new ArrayList<Element>();
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elSynonymyList.addAll(elNomenclature.getChildren("synonomy", nsTaxonx));
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elSynonymyList.addAll(elNomenclature.getChildren("synonymy", nsTaxonx)); //wrong spelling in TaxonX-Schema
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for (Element elSynonymy : elSynonymyList){
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String synonymName = elSynonymy.getChildTextTrim("name");
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if (elSynonymy.getChild("type", nsTaxonx) != null || elSynonymy.getChild("type_loc", nsTaxonx) != null){
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Synonym synonym = getSynonym(config, taxon, synonymName);
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if (synonym != null){
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isChanged |= doNomenclaturalType(config, elSynonymy, nsTaxonx, synonym.getName());
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}
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}
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}
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}
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if (isChanged){
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getTaxonService().save(taxon);
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}
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commitTransaction(tx);
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return;
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}
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private Synonym getSynonym(TaxonXImportConfigurator config, Taxon taxon, String synName){
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Synonym result = null;
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unlazySynonym(config, taxon);
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Set<Synonym> synList = taxon.getSynonyms();
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for (Synonym syn : synList){
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TaxonNameBase<?,?> nameBase = syn.getName();
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if (nameBase != null){
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if (nameBase.isInstanceOf(NonViralName.class)){
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NonViralName<?> nonViralName = nameBase.deproxy(nameBase, NonViralName.class);
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if (nonViralName.getNameCache().equals(synName)){
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return syn; //only first synonym is returned
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}
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}
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}
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}
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logger.warn("Synonym ("+synName+ ")not found for taxon " + taxon.getTitleCache() + getBracketSourceName(config));
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return result;
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}
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private Taxon getTaxon(TaxonXImportConfigurator config){
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Taxon result;
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// result = Taxon.NewInstance(BotanicalName.NewInstance(null), null);
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//ICommonService commonService =config.getCdmAppController().getCommonService();
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ICommonService commonService = getCommonService();
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String originalSourceId = config.getOriginalSourceId();
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String namespace = config.getOriginalSourceTaxonNamespace();
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result = (Taxon)commonService.getSourcedObjectByIdInSource(Taxon.class, originalSourceId , namespace);
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if (result == null){
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logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found");
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}
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean isIgnore(TaxonXImportState state){
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return ! state.getConfig().isDoTypes();
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}
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/**
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*
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* Reads the collection_event tag, creates the according data and stores it.
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* TODO under work
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* @param elNomenclature
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* @param nsTaxonx
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* @param taxonBase
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* @return
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*/
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private boolean doNomenclaturalType(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonNameBase taxonName){
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boolean success = true;
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if (taxonName == null){
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logger.warn("taxonName is null");
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return false;
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}
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if (elNomenclature == null){
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logger.warn("elNomenclature is null");
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return false;
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}
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Element elType = elNomenclature.getChild("type", nsTaxonx);
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Element elTypeLoc = elNomenclature.getChild("type_loc", nsTaxonx);
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if (elType != null || elTypeLoc != null){
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unlazyTypeDesignation(config, taxonName);
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if (taxonName.isInfraGeneric() || taxonName.isSupraGeneric() || taxonName.isGenus()){
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success &= doNameType(elType, taxonName, config);
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}else{
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success &= doSpecimenType(config, elType, elTypeLoc, taxonName);
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}
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return success;
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}
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return false;
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}
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private boolean doSpecimenType(TaxonXImportConfigurator config, Element elType, Element elTypeLoc, TaxonNameBase taxonName){
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Reference citation = null;
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String citationMicroReference = null;
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String originalNameString = null;
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boolean isNotDesignated = true;
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boolean addToAllHomotypicNames = true;
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SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance();
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//elType
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if (elType != null){
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doElType(elType, simpleSpecimen, config);
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}//elType
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//typeLoc
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HashMap<DerivedUnit, SpecimenTypeDesignationStatus> typeLocMap = null;
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if (elTypeLoc != null){
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typeLocMap = doElTypeLoc(elTypeLoc, simpleSpecimen, taxonName, config);
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}
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if (typeLocMap != null && typeLocMap.size() >0){
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for (DerivedUnit specimen : typeLocMap.keySet()){
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SpecimenTypeDesignationStatus status = typeLocMap.get(specimen);
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taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames);
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}
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}else{ // no type_loc
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SpecimenTypeDesignationStatus status = null;
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taxonName.addSpecimenTypeDesignation(simpleSpecimen.getSpecimen(), status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames);
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}
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return true;
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}
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private boolean doElType(Element elType, SimpleSpecimen simpleSpecimen, TaxonXImportConfigurator config){
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//type
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String text = elType.getTextNormalize();
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if (text.endsWith(";")){
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text = text + " ";
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}
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String[] type = text.split(";");
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if (type.length != 3 ){
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if (text.equals("")){
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logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config));
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}else{
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logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));
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}
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simpleSpecimen.setTitleCache(elType.getTextNormalize());
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}else{
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String strLocality = type[0].trim();
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if (! "".equals(strLocality)){
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// simpleSpecimen.setLocality(strLocality);
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}
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String strCollector = type[1].trim();
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if (! "".equals(strCollector)){
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AgentBase collector = Person.NewTitledInstance(strCollector);
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// simpleSpecimen.setCollector(collector);
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}
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String strCollectorNumber = type[2].trim();
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if (! "".equals(strCollectorNumber)){
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// simpleSpecimen.setCollectorsNumber(strCollectorNumber);
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}
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String title = CdmUtils.concat(" ", new String[]{strLocality, strCollector, strCollectorNumber});
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simpleSpecimen.setTitleCache(title);
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}
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return true;
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}
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private boolean doNameType(Element elType, TaxonNameBase taxonName, TaxonXImportConfigurator config){
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boolean success = true;
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//type
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String text = elType.getTextNormalize();
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logger.info("Type: " + text);
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if (text.endsWith(";")){
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text = text + " ";
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}
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String[] type = text.split(";");
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if (type.length != 3 ){
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if (text.equals("")){
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logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config));
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}else{
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logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));
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}
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success = false;
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}else{
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String statusStr = type[0].trim();
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String taxonNameStr = type[1].trim();
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String authorStr = type[2].trim();
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NameTypeDesignationStatus status = getNameTypeStatus(statusStr);
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/*boolean isLectoType = getIsLectoType(statusStr);*/
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// if (status == null){
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// logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));
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// success = false;
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// }else{
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// TaxonNameBase childType = getChildrenNameType(taxonName, taxonNameStr, authorStr);
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// if (childType != null){
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// return doNameTypeDesignation(taxonName, childType, status);
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// }else{
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String[] epis = taxonNameStr.split(" ");
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String uninomial = epis[0].trim();
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String specEpi = epis[1].trim();
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Pager<TaxonNameBase> nameTypes = getNameService().searchNames(uninomial, null, specEpi, null, Rank.SPECIES(), null, null, null, null);
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List<NonViralName> result = new ArrayList<NonViralName>();
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for (TaxonNameBase nt : nameTypes.getRecords()){
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NonViralName nameType = CdmBase.deproxy(nt, NonViralName.class);
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if (compareAuthorship(nameType, authorStr)){
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result.add(nameType);
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success &= doNameTypeDesignation(taxonName, nameType, status/*, isLectoType*/);
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}else{
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//TODO ?
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}
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}
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if (result.size() > 1){
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logger.warn("More than 1 name matches: " + text);
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success = false;
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}else if (result.size() == 0){
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logger.warn("No name matches: " + text + "(" + config.getSourceNameString() + ")");
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success = false;
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}
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// }
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// }
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}
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return success;
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}
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322
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private TaxonNameBase getChildrenNameType(TaxonNameBase name, String typeStr, String authorStr){
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TaxonNameBase result = null;
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Set<TaxonBase> list = name.getTaxonBases();
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for (TaxonBase taxonBase : list){
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Taxon taxon;
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if (taxonBase.isInstanceOf(Taxon.class)){
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taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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}else{
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Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
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taxon = syn.getAcceptedTaxa().iterator().next();
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}
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Set<Taxon> children = taxon.getTaxonomicChildren();
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for (Taxon child: children){
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NonViralName childName = (CdmBase.deproxy(child.getName(), NonViralName.class));
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if (childName.getNameCache().equals(typeStr)){
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if (compareAuthorship(childName, authorStr)){
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return childName;
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}
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}
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342
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}
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343
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}
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return result;
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345
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}
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346
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347
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private boolean compareAuthorship(NonViralName typeName, String authorStr){
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348
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boolean result = false;
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349
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authorStr = authorStr.replaceAll("\\s+and\\s+", "&");
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350
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authorStr = authorStr.replaceAll("\\s*", "");
|
|
351
|
authorStr = authorStr.replaceAll("\\.$", "");
|
|
352
|
String typeCache = typeName.getAuthorshipCache().replaceAll("\\s*", "");
|
|
353
|
typeCache = typeCache.replaceAll("\\.$", "");
|
|
354
|
if (authorStr.equals(typeCache)){
|
|
355
|
return true;
|
|
356
|
}else{
|
|
357
|
logger.info(" Authors different: " + authorStr + " <-> " + typeCache);
|
|
358
|
}
|
|
359
|
return result;
|
|
360
|
}
|
|
361
|
|
|
362
|
private NameTypeDesignationStatus getNameTypeStatus(String statusString){
|
|
363
|
//FIXME some types (not further defined types) do not exist yet
|
|
364
|
if (true){
|
|
365
|
return null;
|
|
366
|
}
|
|
367
|
if (statusString.trim().equalsIgnoreCase("Type")){
|
|
368
|
return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();
|
|
369
|
}else if (statusString.trim().equalsIgnoreCase("Lectotype")){
|
|
370
|
return NameTypeDesignationStatus.LECTOTYPE();
|
|
371
|
}else if (statusString.trim().equalsIgnoreCase("Holotype")){
|
|
372
|
logger.warn("Holotype does not yet exist in CDM");
|
|
373
|
return NameTypeDesignationStatus.NOT_APPLICABLE();
|
|
374
|
}else if (statusString.trim().equalsIgnoreCase("paratype")){
|
|
375
|
logger.warn("paratype does not yet exist in CDM");
|
|
376
|
return NameTypeDesignationStatus.NOT_APPLICABLE();
|
|
377
|
}
|
|
378
|
else{
|
|
379
|
logger.warn("Status not recognized: " + statusString);
|
|
380
|
return null;
|
|
381
|
}
|
|
382
|
}
|
|
383
|
|
|
384
|
private boolean getIsLectoType(String statusString){
|
|
385
|
//FIXME may be deleted once getNameTypeStatus works finde
|
|
386
|
if (statusString.trim().equals("Lectotype")){
|
|
387
|
return true;
|
|
388
|
}else{
|
|
389
|
return false;
|
|
390
|
}
|
|
391
|
}
|
|
392
|
|
|
393
|
|
|
394
|
private boolean doNameTypeDesignation(TaxonNameBase name, TaxonNameBase type, NameTypeDesignationStatus status/*, boolean isLectoType*/){
|
|
395
|
Reference citation = null;
|
|
396
|
String citationMicroReference = null;
|
|
397
|
String originalNameString = null;
|
|
398
|
boolean addToAllHomotypicNames = true;
|
|
399
|
|
|
400
|
// name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString, status, addToAllHomotypicNames);
|
|
401
|
name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString,status, false, false, /*isLectoType, */false, addToAllHomotypicNames);
|
|
402
|
return true;
|
|
403
|
}
|
|
404
|
|
|
405
|
/**
|
|
406
|
* Reads the typeLoc element split in parts for eacht type (holo, iso,...)
|
|
407
|
* @param elTypeLoc
|
|
408
|
* @param simpleSpecimen
|
|
409
|
* @param taxonName
|
|
410
|
* @param config
|
|
411
|
* @return
|
|
412
|
*/
|
|
413
|
private HashMap<DerivedUnit, SpecimenTypeDesignationStatus> doElTypeLoc(Element elTypeLoc,
|
|
414
|
SimpleSpecimen simpleSpecimen,
|
|
415
|
TaxonNameBase<?,?> taxonName,
|
|
416
|
TaxonXImportConfigurator config){
|
|
417
|
|
|
418
|
HashMap<DerivedUnit, SpecimenTypeDesignationStatus> result = new HashMap<DerivedUnit, SpecimenTypeDesignationStatus>();
|
|
419
|
|
|
420
|
String typeLocFullString = elTypeLoc.getTextTrim();
|
|
421
|
typeLocFullString = typeLocFullString.replace("(", "").replace(")", "");
|
|
422
|
String[] typeLocStatusList = typeLocFullString.split(";");
|
|
423
|
|
|
424
|
DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen();
|
|
425
|
|
|
426
|
|
|
427
|
for (String typeLocStatus : typeLocStatusList){
|
|
428
|
typeLocStatus = typeLocStatus.trim();
|
|
429
|
int pos = typeLocStatus.indexOf(" ");
|
|
430
|
if (pos == -1){
|
|
431
|
logger.warn("Unknown format or empty type_loc : '" +typeLocStatus + "'" + getBracketSourceName(config));
|
|
432
|
result.put(originalSpecimen, null);
|
|
433
|
}else{
|
|
434
|
String statusString = typeLocStatus.substring(0,pos);
|
|
435
|
SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config);
|
|
436
|
//TODO
|
|
437
|
//String[] collectionStrings = typeLocStatus.substring(pos).split(",");
|
|
438
|
String tmpCollString = typeLocStatus.substring(pos).trim();
|
|
439
|
//for(String collectionString : collectionStrings){
|
|
440
|
if (tmpCollString.contains("typ")){
|
|
441
|
logger.warn("Is this really only a collection string? : " + tmpCollString + getBracketSourceName(config));
|
|
442
|
}
|
|
443
|
DerivedUnit specimen;
|
|
444
|
specimen = (DerivedUnit)originalSpecimen.clone();
|
|
445
|
String title = originalSpecimen.getTitleCache();
|
|
446
|
title = title + "(" + tmpCollString + ")";
|
|
447
|
specimen.setTitleCache(title, true );
|
|
448
|
result.put(specimen, status);
|
|
449
|
//}
|
|
450
|
}
|
|
451
|
}
|
|
452
|
|
|
453
|
return result;
|
|
454
|
}
|
|
455
|
|
|
456
|
/**
|
|
457
|
*
|
|
458
|
* Reads the collection_event tag, creates the according data and stores it.
|
|
459
|
* TODO under work
|
|
460
|
* @param elNomenclature
|
|
461
|
* @param nsTaxonx
|
|
462
|
* @param taxonBase
|
|
463
|
* @return
|
|
464
|
*/
|
|
465
|
private boolean doCollectionEvent(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonBase taxonBase){
|
|
466
|
boolean result = false;
|
|
467
|
if (elNomenclature == null){
|
|
468
|
return false;
|
|
469
|
}
|
|
470
|
Element elCollectionEvent = elNomenclature.getChild("collection_event", nsTaxonx);
|
|
471
|
if (elCollectionEvent == null){
|
|
472
|
return result;
|
|
473
|
}
|
|
474
|
Element elLocality = elCollectionEvent.getChild("locality", nsTaxonx);
|
|
475
|
Element elType = elCollectionEvent.getChild("type", nsTaxonx);
|
|
476
|
Element elTypeLoc = elCollectionEvent.getChild("type_loc", nsTaxonx);
|
|
477
|
|
|
478
|
//locality
|
|
479
|
SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance();
|
|
480
|
String locality = elLocality.getTextNormalize();
|
|
481
|
if (! "".equals(locality)){
|
|
482
|
simpleSpecimen.setLocality(locality);
|
|
483
|
}
|
|
484
|
|
|
485
|
//type
|
|
486
|
String[] type = elType.getTextNormalize().split(" ");
|
|
487
|
if (type.length != 2 ){
|
|
488
|
logger.warn("<collecion_even><type> is of unsupported format: " + elType.getTextNormalize());
|
|
489
|
}else{
|
|
490
|
AgentBase collector = Person.NewTitledInstance(type[0]);
|
|
491
|
simpleSpecimen.setCollector(collector);
|
|
492
|
|
|
493
|
String collectorNumber = type[1];
|
|
494
|
simpleSpecimen.setCollectorsNumber(collectorNumber);
|
|
495
|
}
|
|
496
|
|
|
497
|
//typeLoc
|
|
498
|
String typeLocFullString = elTypeLoc.getTextTrim();
|
|
499
|
typeLocFullString = typeLocFullString.replace("(", "").replace(")", "");
|
|
500
|
String[] typeLocStatusList = typeLocFullString.split(";");
|
|
501
|
|
|
502
|
DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen();
|
|
503
|
|
|
504
|
//TODO special character ?, �, !
|
|
505
|
|
|
506
|
for (String typeLocStatus : typeLocStatusList){
|
|
507
|
typeLocStatus = typeLocStatus.trim();
|
|
508
|
int pos = typeLocStatus.indexOf(" ");
|
|
509
|
if (pos == -1){
|
|
510
|
logger.warn("Unknown format: " + typeLocStatus);
|
|
511
|
}else{
|
|
512
|
String statusString = typeLocStatus.substring(0,pos);
|
|
513
|
SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config);
|
|
514
|
String[] collectionStrings = typeLocStatus.substring(pos).split(",");
|
|
515
|
for(String collectionString : collectionStrings){
|
|
516
|
if (taxonBase != null){
|
|
517
|
TaxonNameBase<?, ?> taxonName = taxonBase.getName();
|
|
518
|
if (taxonName != null){
|
|
519
|
Reference citation = null;
|
|
520
|
String citationMicroReference = null;
|
|
521
|
String originalNameString = null;
|
|
522
|
boolean isNotDesignated = true;
|
|
523
|
boolean addToAllHomotypicNames = true;
|
|
524
|
DerivedUnit specimen = (DerivedUnit)originalSpecimen.clone();
|
|
525
|
unlazyTypeDesignation(config, taxonName);
|
|
526
|
taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames);
|
|
527
|
result = true;
|
|
528
|
}
|
|
529
|
}
|
|
530
|
}
|
|
531
|
}
|
|
532
|
}
|
|
533
|
return result;
|
|
534
|
}
|
|
535
|
|
|
536
|
|
|
537
|
private static Map<String, SpecimenTypeDesignationStatus> statusMap;
|
|
538
|
private static void fillTypeStatusMap(){
|
|
539
|
statusMap = new HashMap<String, SpecimenTypeDesignationStatus>();
|
|
540
|
statusMap.put("epitype", SpecimenTypeDesignationStatus.EPITYPE());
|
|
541
|
statusMap.put("holotype", SpecimenTypeDesignationStatus.HOLOTYPE());
|
|
542
|
statusMap.put("iconotype", SpecimenTypeDesignationStatus.ICONOTYPE());
|
|
543
|
statusMap.put("isotype", SpecimenTypeDesignationStatus.ISOTYPE());
|
|
544
|
statusMap.put("isoneotype", SpecimenTypeDesignationStatus.ISONEOTYPE());
|
|
545
|
statusMap.put("isosyntype", SpecimenTypeDesignationStatus.ISOSYNTYPE());
|
|
546
|
statusMap.put("isolectotype", SpecimenTypeDesignationStatus.ISOLECTOTYPE());
|
|
547
|
statusMap.put("lectotype", SpecimenTypeDesignationStatus.LECTOTYPE());
|
|
548
|
statusMap.put("syntype", SpecimenTypeDesignationStatus.SYNTYPE());
|
|
549
|
statusMap.put("paratype", SpecimenTypeDesignationStatus.PARATYPE());
|
|
550
|
statusMap.put("neotype", SpecimenTypeDesignationStatus.NEOTYPE());
|
|
551
|
statusMap.put("isoepitype", SpecimenTypeDesignationStatus.ISOEPITYPE());
|
|
552
|
statusMap.put("originalmaterial", SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL());
|
|
553
|
statusMap.put("paralectotype", SpecimenTypeDesignationStatus.PARALECTOTYPE());
|
|
554
|
statusMap.put("paraneotype", SpecimenTypeDesignationStatus.PARANEOTYPE());
|
|
555
|
statusMap.put("phototype", SpecimenTypeDesignationStatus.PHOTOTYPE());
|
|
556
|
statusMap.put("secondsteplectotype", SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE());
|
|
557
|
statusMap.put("secondstepneotype", SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE());
|
|
558
|
statusMap.put("type", null);
|
|
559
|
}
|
|
560
|
|
|
561
|
|
|
562
|
//TODO move to TypeDesignation class
|
|
563
|
/**
|
|
564
|
* Returns the typeDesignationStatus according to a type designation status string
|
|
565
|
* @param statusString
|
|
566
|
* @return TypeDesignationStatus
|
|
567
|
*/
|
|
568
|
private static SpecimenTypeDesignationStatus getStatusByStatusString(String statusString, TaxonXImportConfigurator config){
|
|
569
|
SpecimenTypeDesignationStatus result = null;
|
|
570
|
if (statusString == null || "".equals(statusString.trim())){
|
|
571
|
return null;
|
|
572
|
}
|
|
573
|
statusString = statusString.trim().toLowerCase();
|
|
574
|
statusString = statusString.replace("typi", "typus");
|
|
575
|
statusString = statusString.replace("typus", "type");
|
|
576
|
statusString = statusString.replace("types", "type");
|
|
577
|
statusString = statusString.toLowerCase();
|
|
578
|
|
|
579
|
if (statusMap == null){
|
|
580
|
fillTypeStatusMap();
|
|
581
|
}
|
|
582
|
result = statusMap.get(statusString);
|
|
583
|
if (statusString.equals("type")){
|
|
584
|
logger.info("No type designation type" + getBracketSourceName(config));
|
|
585
|
}else if (result == null){
|
|
586
|
logger.warn("Unknown type status string: " + statusString + getBracketSourceName(config));
|
|
587
|
}
|
|
588
|
return result;
|
|
589
|
}
|
|
590
|
|
|
591
|
|
|
592
|
/**
|
|
593
|
* TODO Preliminary to avoid laizy loading errors
|
|
594
|
*/
|
|
595
|
private void unlazyTypeDesignation(TaxonXImportConfigurator config, TaxonNameBase taxonNameBase){
|
|
596
|
TransactionStatus txStatus = startTransaction();
|
|
597
|
//INameService taxonNameService = config.getCdmAppController().getNameService();
|
|
598
|
INameService taxonNameService = getNameService();
|
|
599
|
|
|
600
|
taxonNameService.save(taxonNameBase);
|
|
601
|
Set<TaxonNameBase> typifiedNames = taxonNameBase.getHomotypicalGroup().getTypifiedNames();
|
|
602
|
for(TaxonNameBase typifiedName: typifiedNames){
|
|
603
|
typifiedName.getTypeDesignations().size();
|
|
604
|
}
|
|
605
|
//taxonNameService.saveTaxonName(taxonNameBase);
|
|
606
|
commitTransaction(txStatus);
|
|
607
|
}
|
|
608
|
|
|
609
|
/**
|
|
610
|
* TODO Preliminary to avoid laizy loading errors
|
|
611
|
*/
|
|
612
|
private void unlazySynonym(IImportConfigurator config, Taxon taxon){
|
|
613
|
TransactionStatus txStatus = startTransaction();
|
|
614
|
ITaxonService taxonService = getTaxonService();
|
|
615
|
taxonService.save(taxon);
|
|
616
|
Set<Synonym> synonyms = taxon.getSynonyms();
|
|
617
|
logger.debug(synonyms.size());
|
|
618
|
//taxonService.saveTaxon(taxon);
|
|
619
|
commitTransaction(txStatus);
|
|
620
|
}
|
|
621
|
|
|
622
|
private static String getBracketSourceName(TaxonXImportConfigurator config){
|
|
623
|
return "(" + config.getSourceNameString() + ")";
|
|
624
|
}
|
|
625
|
|
|
626
|
|
|
627
|
}
|