Revision cdda449c
Added by Andreas Müller almost 2 years ago
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXNomenclatureImport.java | ||
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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.logging.log4j.LogManager;import org.apache.logging.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.CdmImportBase; |
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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.name.INonViralName; |
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
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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.TaxonName; |
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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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* @since 29.07.2008 |
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*/ |
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@Component |
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public class TaxonXNomenclatureImport |
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extends CdmImportBase<TaxonXImportConfigurator, TaxonXImportState> { |
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private static final long serialVersionUID = 796115831082828758L; |
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private static final Logger logger = LogManager.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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TaxonName nameBase = syn.getName(); |
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if (nameBase != null){ |
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if (nameBase.isNonViral()){ |
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if (nameBase.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(TaxonNameFactory.NewBotanicalInstance(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 = 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, TaxonName 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, TaxonName 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, TaxonName 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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// TaxonName 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<TaxonName> nameTypes = getNameService().searchNames(uninomial, null, specEpi, null, Rank.SPECIES(), null, null, null, null); |
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List<INonViralName> result = new ArrayList<>(); |
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for (TaxonName nt : nameTypes.getRecords()){ |
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if (compareAuthorship(nt, authorStr)){ |
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result.add(nt); |
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success &= doNameTypeDesignation(taxonName, nt, 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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// private TaxonName getChildrenNameType(TaxonName name, String typeStr, String authorStr){ |
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// TaxonName 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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// INonViralName childName = child.getName(); |
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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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// } |
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// } |
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// return result; |
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// } |
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private boolean compareAuthorship(INonViralName typeName, String authorStr){ |
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boolean result = false; |
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authorStr = authorStr.replaceAll("\\s+and\\s+", "&"); |
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authorStr = authorStr.replaceAll("\\s*", ""); |
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authorStr = authorStr.replaceAll("\\.$", ""); |
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String typeCache = typeName.getAuthorshipCache().replaceAll("\\s*", ""); |
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typeCache = typeCache.replaceAll("\\.$", ""); |
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if (authorStr.equals(typeCache)){ |
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return true; |
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}else{ |
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logger.info(" Authors different: " + authorStr + " <-> " + typeCache); |
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} |
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return result; |
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} |
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private NameTypeDesignationStatus getNameTypeStatus(String statusString){ |
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//FIXME some types (not further defined types) do not exist yet |
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if (true){ |
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return null; |
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} |
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if (statusString.trim().equalsIgnoreCase("Type")){ |
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return NameTypeDesignationStatus.ORIGINAL_DESIGNATION(); |
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}else if (statusString.trim().equalsIgnoreCase("Lectotype")){ |
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return NameTypeDesignationStatus.LECTOTYPE(); |
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}else if (statusString.trim().equalsIgnoreCase("Holotype")){ |
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logger.warn("Holotype does not yet exist in CDM"); |
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return NameTypeDesignationStatus.NOT_APPLICABLE(); |
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}else if (statusString.trim().equalsIgnoreCase("paratype")){ |
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logger.warn("paratype does not yet exist in CDM"); |
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return NameTypeDesignationStatus.NOT_APPLICABLE(); |
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} |
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else{ |
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logger.warn("Status not recognized: " + statusString); |
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return null; |
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} |
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} |
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private boolean getIsLectoType(String statusString){ |
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//FIXME may be deleted once getNameTypeStatus works finde |
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if (statusString.trim().equals("Lectotype")){ |
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return true; |
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}else{ |
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return false; |
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} |
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} |
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private boolean doNameTypeDesignation(TaxonName name, TaxonName type, NameTypeDesignationStatus status/*, boolean isLectoType*/){ |
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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 addToAllHomotypicNames = true; |
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// name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString, status, addToAllHomotypicNames); |
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name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString,status, false, false, /*isLectoType, */false, addToAllHomotypicNames); |
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return true; |
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} |
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/** |
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* Reads the typeLoc element split in parts for eacht type (holo, iso,...) |
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* @param elTypeLoc |
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* @param simpleSpecimen |
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* @param taxonName |
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* @param config |
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* @return |
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*/ |
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private HashMap<DerivedUnit, SpecimenTypeDesignationStatus> doElTypeLoc(Element elTypeLoc, |
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SimpleSpecimen simpleSpecimen, |
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TaxonName taxonName, |
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TaxonXImportConfigurator config){ |
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HashMap<DerivedUnit, SpecimenTypeDesignationStatus> result = new HashMap<DerivedUnit, SpecimenTypeDesignationStatus>(); |
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String typeLocFullString = elTypeLoc.getTextTrim(); |
|
419 |
typeLocFullString = typeLocFullString.replace("(", "").replace(")", ""); |
|
420 |
String[] typeLocStatusList = typeLocFullString.split(";"); |
|
421 |
|
|
422 |
DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen(); |
|
423 |
|
|
424 |
|
|
425 |
for (String typeLocStatus : typeLocStatusList){ |
|
426 |
typeLocStatus = typeLocStatus.trim(); |
|
427 |
int pos = typeLocStatus.indexOf(" "); |
|
428 |
if (pos == -1){ |
|
429 |
logger.warn("Unknown format or empty type_loc : '" +typeLocStatus + "'" + getBracketSourceName(config)); |
|
430 |
result.put(originalSpecimen, null); |
|
431 |
}else{ |
|
432 |
String statusString = typeLocStatus.substring(0,pos); |
|
433 |
SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config); |
|
434 |
//TODO |
|
435 |
//String[] collectionStrings = typeLocStatus.substring(pos).split(","); |
|
436 |
String tmpCollString = typeLocStatus.substring(pos).trim(); |
|
437 |
//for(String collectionString : collectionStrings){ |
|
438 |
if (tmpCollString.contains("typ")){ |
|
439 |
logger.warn("Is this really only a collection string? : " + tmpCollString + getBracketSourceName(config)); |
|
440 |
} |
|
441 |
DerivedUnit specimen; |
|
442 |
specimen = (DerivedUnit)originalSpecimen.clone(); |
|
443 |
String title = originalSpecimen.getTitleCache(); |
|
444 |
title = title + "(" + tmpCollString + ")"; |
|
445 |
specimen.setTitleCache(title, true ); |
|
446 |
result.put(specimen, status); |
|
447 |
//} |
|
448 |
} |
|
449 |
} |
|
450 |
|
|
451 |
return result; |
|
452 |
} |
|
453 |
|
|
454 |
/** |
|
455 |
* |
|
456 |
* Reads the collection_event tag, creates the according data and stores it. |
|
457 |
* TODO under work |
|
458 |
* @param elNomenclature |
|
459 |
* @param nsTaxonx |
|
460 |
* @param taxonBase |
|
461 |
* @return |
|
462 |
*/ |
|
463 |
private boolean doCollectionEvent(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonBase taxonBase){ |
|
464 |
boolean result = false; |
|
465 |
if (elNomenclature == null){ |
|
466 |
return false; |
|
467 |
} |
|
468 |
Element elCollectionEvent = elNomenclature.getChild("collection_event", nsTaxonx); |
|
469 |
if (elCollectionEvent == null){ |
|
470 |
return result; |
|
471 |
} |
|
472 |
Element elLocality = elCollectionEvent.getChild("locality", nsTaxonx); |
|
473 |
Element elType = elCollectionEvent.getChild("type", nsTaxonx); |
|
474 |
Element elTypeLoc = elCollectionEvent.getChild("type_loc", nsTaxonx); |
|
475 |
|
|
476 |
//locality |
|
477 |
SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance(); |
|
478 |
String locality = elLocality.getTextNormalize(); |
|
479 |
if (! "".equals(locality)){ |
|
480 |
simpleSpecimen.setLocality(locality); |
|
481 |
} |
|
482 |
|
|
483 |
//type |
|
484 |
String[] type = elType.getTextNormalize().split(" "); |
|
485 |
if (type.length != 2 ){ |
|
486 |
logger.warn("<collecion_even><type> is of unsupported format: " + elType.getTextNormalize()); |
|
487 |
}else{ |
|
488 |
AgentBase collector = Person.NewTitledInstance(type[0]); |
|
489 |
simpleSpecimen.setCollector(collector); |
|
490 |
|
|
491 |
String collectorNumber = type[1]; |
|
492 |
simpleSpecimen.setCollectorsNumber(collectorNumber); |
|
493 |
} |
|
494 |
|
|
495 |
//typeLoc |
|
496 |
String typeLocFullString = elTypeLoc.getTextTrim(); |
|
497 |
typeLocFullString = typeLocFullString.replace("(", "").replace(")", ""); |
|
498 |
String[] typeLocStatusList = typeLocFullString.split(";"); |
|
499 |
|
|
500 |
DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen(); |
|
501 |
|
|
502 |
//TODO special character ?, �, ! |
|
503 |
|
|
504 |
for (String typeLocStatus : typeLocStatusList){ |
|
505 |
typeLocStatus = typeLocStatus.trim(); |
|
506 |
int pos = typeLocStatus.indexOf(" "); |
|
507 |
if (pos == -1){ |
|
508 |
logger.warn("Unknown format: " + typeLocStatus); |
|
509 |
}else{ |
|
510 |
String statusString = typeLocStatus.substring(0,pos); |
|
511 |
SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config); |
|
512 |
String[] collectionStrings = typeLocStatus.substring(pos).split(","); |
|
513 |
for(String collectionString : collectionStrings){ |
|
514 |
if (taxonBase != null){ |
|
515 |
TaxonName taxonName = taxonBase.getName(); |
|
516 |
if (taxonName != null){ |
|
517 |
Reference citation = null; |
|
518 |
String citationMicroReference = null; |
|
519 |
String originalNameString = null; |
|
520 |
boolean isNotDesignated = true; |
|
521 |
boolean addToAllHomotypicNames = true; |
|
522 |
DerivedUnit specimen = (DerivedUnit)originalSpecimen.clone(); |
|
523 |
unlazyTypeDesignation(config, taxonName); |
|
524 |
taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames); |
|
525 |
result = true; |
|
526 |
} |
|
527 |
} |
|
528 |
} |
|
529 |
} |
|
530 |
} |
|
531 |
return result; |
|
532 |
} |
|
533 |
|
|
534 |
|
|
535 |
private static Map<String, SpecimenTypeDesignationStatus> statusMap; |
|
536 |
private static void fillTypeStatusMap(){ |
|
537 |
statusMap = new HashMap<String, SpecimenTypeDesignationStatus>(); |
|
538 |
statusMap.put("epitype", SpecimenTypeDesignationStatus.EPITYPE()); |
|
539 |
statusMap.put("holotype", SpecimenTypeDesignationStatus.HOLOTYPE()); |
|
540 |
statusMap.put("iconotype", SpecimenTypeDesignationStatus.ICONOTYPE()); |
|
541 |
statusMap.put("isotype", SpecimenTypeDesignationStatus.ISOTYPE()); |
|
542 |
statusMap.put("isoneotype", SpecimenTypeDesignationStatus.ISONEOTYPE()); |
|
543 |
statusMap.put("isosyntype", SpecimenTypeDesignationStatus.ISOSYNTYPE()); |
|
544 |
statusMap.put("isolectotype", SpecimenTypeDesignationStatus.ISOLECTOTYPE()); |
|
545 |
statusMap.put("lectotype", SpecimenTypeDesignationStatus.LECTOTYPE()); |
|
546 |
statusMap.put("syntype", SpecimenTypeDesignationStatus.SYNTYPE()); |
|
547 |
statusMap.put("paratype", SpecimenTypeDesignationStatus.PARATYPE()); |
|
548 |
statusMap.put("neotype", SpecimenTypeDesignationStatus.NEOTYPE()); |
|
549 |
statusMap.put("isoepitype", SpecimenTypeDesignationStatus.ISOEPITYPE()); |
|
550 |
statusMap.put("originalmaterial", SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL()); |
|
551 |
statusMap.put("paralectotype", SpecimenTypeDesignationStatus.PARALECTOTYPE()); |
|
552 |
statusMap.put("paraneotype", SpecimenTypeDesignationStatus.PARANEOTYPE()); |
|
553 |
statusMap.put("phototype", SpecimenTypeDesignationStatus.PHOTOTYPE()); |
|
554 |
statusMap.put("secondsteplectotype", SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE()); |
|
555 |
statusMap.put("secondstepneotype", SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE()); |
|
556 |
statusMap.put("type", null); |
|
557 |
} |
|
558 |
|
|
559 |
|
|
560 |
//TODO move to TypeDesignation class |
|
561 |
/** |
|
562 |
* Returns the typeDesignationStatus according to a type designation status string |
|
563 |
* @param statusString |
|
564 |
* @return TypeDesignationStatus |
|
565 |
*/ |
|
566 |
private static SpecimenTypeDesignationStatus getStatusByStatusString(String statusString, TaxonXImportConfigurator config){ |
|
567 |
SpecimenTypeDesignationStatus result = null; |
|
568 |
if (statusString == null || "".equals(statusString.trim())){ |
|
569 |
return null; |
|
570 |
} |
|
571 |
statusString = statusString.trim().toLowerCase(); |
|
572 |
statusString = statusString.replace("typi", "typus"); |
|
573 |
statusString = statusString.replace("typus", "type"); |
|
574 |
statusString = statusString.replace("types", "type"); |
|
575 |
statusString = statusString.toLowerCase(); |
|
576 |
|
|
577 |
if (statusMap == null){ |
|
578 |
fillTypeStatusMap(); |
|
579 |
} |
|
580 |
result = statusMap.get(statusString); |
|
581 |
if (statusString.equals("type")){ |
|
582 |
logger.info("No type designation type" + getBracketSourceName(config)); |
|
583 |
}else if (result == null){ |
|
584 |
logger.warn("Unknown type status string: " + statusString + getBracketSourceName(config)); |
|
585 |
} |
|
586 |
return result; |
|
587 |
} |
|
588 |
|
|
589 |
|
|
590 |
/** |
|
591 |
* TODO Preliminary to avoid laizy loading errors |
|
592 |
*/ |
|
593 |
private void unlazyTypeDesignation(TaxonXImportConfigurator config, TaxonName taxonName){ |
|
594 |
TransactionStatus txStatus = startTransaction(); |
|
595 |
//INameService taxonNameService = config.getCdmAppController().getNameService(); |
|
596 |
INameService taxonNameService = getNameService(); |
|
597 |
|
|
598 |
taxonNameService.save(taxonName); |
|
599 |
Set<TaxonName> typifiedNames = taxonName.getHomotypicalGroup().getTypifiedNames(); |
|
600 |
for(TaxonName typifiedName: typifiedNames){ |
|
601 |
typifiedName.getTypeDesignations().size(); |
|
602 |
} |
|
603 |
//taxonNameService.saveTaxonName(taxonName); |
|
604 |
commitTransaction(txStatus); |
|
605 |
} |
|
606 |
|
|
607 |
/** |
|
608 |
* TODO Preliminary to avoid laizy loading errors |
|
609 |
*/ |
|
610 |
private void unlazySynonym(IImportConfigurator config, Taxon taxon){ |
|
611 |
TransactionStatus txStatus = startTransaction(); |
|
612 |
ITaxonService taxonService = getTaxonService(); |
|
613 |
taxonService.save(taxon); |
|
614 |
Set<Synonym> synonyms = taxon.getSynonyms(); |
|
615 |
logger.debug(synonyms.size()); |
|
616 |
//taxonService.saveTaxon(taxon); |
|
617 |
commitTransaction(txStatus); |
|
618 |
} |
|
619 |
|
|
620 |
private static String getBracketSourceName(TaxonXImportConfigurator config){ |
|
621 |
return "(" + config.getSourceNameString() + ")"; |
|
622 |
} |
|
623 |
|
|
624 |
|
|
625 |
} |
|
1 |
/** |
|
2 |
* Copyright (C) 2007 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.cdm.io.taxonx; |
|
10 |
|
|
11 |
import java.util.ArrayList; |
|
12 |
import java.util.HashMap; |
|
13 |
import java.util.List; |
|
14 |
import java.util.Map; |
|
15 |
import java.util.Set; |
|
16 |
|
|
17 |
import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger; |
|
18 |
import org.jdom.Element; |
|
19 |
import org.jdom.Namespace; |
|
20 |
import org.springframework.stereotype.Component; |
|
21 |
import org.springframework.transaction.TransactionStatus; |
|
22 |
|
|
23 |
import eu.etaxonomy.cdm.api.service.ICommonService; |
|
24 |
import eu.etaxonomy.cdm.api.service.INameService; |
|
25 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
|
26 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
|
27 |
import eu.etaxonomy.cdm.common.CdmUtils; |
|
28 |
import eu.etaxonomy.cdm.io.common.CdmImportBase; |
|
29 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
30 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
|
31 |
import eu.etaxonomy.cdm.model.agent.Person; |
|
32 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
|
33 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
|
34 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
35 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
|
36 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
37 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
38 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
39 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
40 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
41 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
42 |
|
|
43 |
|
|
44 |
/** |
|
45 |
* @author a.mueller |
|
46 |
* @since 29.07.2008 |
|
47 |
*/ |
|
48 |
@Component |
|
49 |
public class TaxonXNomenclatureImport |
|
50 |
extends CdmImportBase<TaxonXImportConfigurator, TaxonXImportState> { |
|
51 |
|
|
52 |
private static final long serialVersionUID = 796115831082828758L; |
|
53 |
private static final Logger logger = LogManager.getLogger(TaxonXNomenclatureImport.class); |
|
54 |
|
|
55 |
@SuppressWarnings("unused") |
|
56 |
private static int modCount = 10000; |
|
57 |
|
|
58 |
public TaxonXNomenclatureImport(){ |
|
59 |
super(); |
|
60 |
} |
|
61 |
|
|
62 |
@Override |
|
63 |
public boolean doCheck(TaxonXImportState state){ |
|
64 |
boolean result = true; |
|
65 |
logger.warn("Checking for Types not yet implemented"); |
|
66 |
//result &= checkArticlesWithoutJournal(bmiConfig); |
|
67 |
//result &= checkPartOfJournal(bmiConfig); |
|
68 |
|
|
69 |
return result; |
|
70 |
} |
|
71 |
|
|
72 |
@Override |
|
73 |
public void doInvoke(TaxonXImportState state){ |
|
74 |
logger.info("start make Nomenclature ..."); |
|
75 |
TransactionStatus tx = startTransaction(); |
|
76 |
TaxonXImportConfigurator config = state.getConfig(); |
|
77 |
Element root = config.getSourceRoot(); |
|
78 |
Namespace nsTaxonx = root.getNamespace(); |
|
79 |
|
|
80 |
//for testing only |
|
81 |
Taxon taxon = getTaxon(config); |
|
82 |
boolean isChanged = false; |
|
83 |
|
|
84 |
Element elTaxonBody = root.getChild("taxonxBody", nsTaxonx); |
|
85 |
Element elTreatment = elTaxonBody.getChild("treatment", nsTaxonx); |
|
86 |
Element elNomenclature = elTreatment.getChild("nomenclature", nsTaxonx); |
|
87 |
|
|
88 |
//isChanged |= doCollectionEvent(txConfig, elNomenclature, nsTaxonx, taxon); |
|
89 |
|
|
90 |
if (taxon != null && taxon.getName() != null && elNomenclature != null){ |
|
91 |
isChanged |= doNomenclaturalType(config, elNomenclature, nsTaxonx, taxon.getName()); |
|
92 |
List<Element> elSynonymyList = new ArrayList<Element>(); |
|
93 |
elSynonymyList.addAll(elNomenclature.getChildren("synonomy", nsTaxonx)); |
|
94 |
elSynonymyList.addAll(elNomenclature.getChildren("synonymy", nsTaxonx)); //wrong spelling in TaxonX-Schema |
|
95 |
for (Element elSynonymy : elSynonymyList){ |
|
96 |
String synonymName = elSynonymy.getChildTextTrim("name"); |
|
97 |
if (elSynonymy.getChild("type", nsTaxonx) != null || elSynonymy.getChild("type_loc", nsTaxonx) != null){ |
|
98 |
Synonym synonym = getSynonym(config, taxon, synonymName); |
|
99 |
if (synonym != null){ |
|
100 |
isChanged |= doNomenclaturalType(config, elSynonymy, nsTaxonx, synonym.getName()); |
|
101 |
} |
|
102 |
} |
|
103 |
} |
|
104 |
} |
|
105 |
|
|
106 |
|
|
107 |
if (isChanged){ |
|
108 |
getTaxonService().save(taxon); |
|
109 |
} |
|
110 |
commitTransaction(tx); |
|
111 |
return; |
|
112 |
} |
|
113 |
|
|
114 |
private Synonym getSynonym(TaxonXImportConfigurator config, Taxon taxon, String synName){ |
|
115 |
Synonym result = null; |
|
116 |
unlazySynonym(config, taxon); |
|
117 |
Set<Synonym> synList = taxon.getSynonyms(); |
|
118 |
for (Synonym syn : synList){ |
|
119 |
TaxonName nameBase = syn.getName(); |
|
120 |
if (nameBase != null){ |
|
121 |
if (nameBase.isNonViral()){ |
|
122 |
if (nameBase.getNameCache().equals(synName)){ |
|
123 |
return syn; //only first synonym is returned |
|
124 |
} |
|
125 |
} |
|
126 |
} |
|
127 |
} |
|
128 |
logger.warn("Synonym ("+synName+ ")not found for taxon " + taxon.getTitleCache() + getBracketSourceName(config)); |
|
129 |
return result; |
|
130 |
} |
|
131 |
|
|
132 |
private Taxon getTaxon(TaxonXImportConfigurator config){ |
|
133 |
Taxon result; |
|
134 |
// result = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(null), null); |
|
135 |
//ICommonService commonService =config.getCdmAppController().getCommonService(); |
|
136 |
ICommonService commonService = getCommonService(); |
|
137 |
String originalSourceId = config.getOriginalSourceId(); |
|
138 |
String namespace = config.getOriginalSourceTaxonNamespace(); |
|
139 |
result = commonService.getSourcedObjectByIdInSource(Taxon.class, originalSourceId , namespace); |
|
140 |
if (result == null){ |
|
141 |
logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found"); |
|
142 |
} |
|
143 |
return result; |
|
144 |
} |
|
145 |
|
|
146 |
/* (non-Javadoc) |
|
147 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
148 |
*/ |
|
149 |
@Override |
|
150 |
protected boolean isIgnore(TaxonXImportState state){ |
|
151 |
return ! state.getConfig().isDoTypes(); |
|
152 |
} |
|
153 |
|
|
154 |
/** |
|
155 |
* |
|
156 |
* Reads the collection_event tag, creates the according data and stores it. |
|
157 |
* TODO under work |
|
158 |
* @param elNomenclature |
|
159 |
* @param nsTaxonx |
|
160 |
* @param taxonBase |
|
161 |
* @return |
|
162 |
*/ |
|
163 |
private boolean doNomenclaturalType(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonName taxonName){ |
|
164 |
boolean success = true; |
|
165 |
if (taxonName == null){ |
|
166 |
logger.warn("taxonName is null"); |
|
167 |
return false; |
|
168 |
} |
|
169 |
if (elNomenclature == null){ |
|
170 |
logger.warn("elNomenclature is null"); |
|
171 |
return false; |
|
172 |
} |
|
173 |
|
|
174 |
|
|
175 |
Element elType = elNomenclature.getChild("type", nsTaxonx); |
|
176 |
Element elTypeLoc = elNomenclature.getChild("type_loc", nsTaxonx); |
|
177 |
|
|
178 |
if (elType != null || elTypeLoc != null){ |
|
179 |
unlazyTypeDesignation(config, taxonName); |
|
180 |
|
|
181 |
if (taxonName.isInfraGeneric() || taxonName.isSupraGeneric() || taxonName.isGenus()){ |
|
182 |
success &= doNameType(elType, taxonName, config); |
|
183 |
}else{ |
|
184 |
success &= doSpecimenType(config, elType, elTypeLoc, taxonName); |
|
185 |
|
|
186 |
|
|
187 |
} |
|
188 |
return success; |
|
189 |
} |
|
190 |
return false; |
|
191 |
} |
|
192 |
|
|
193 |
|
|
194 |
private boolean doSpecimenType(TaxonXImportConfigurator config, Element elType, Element elTypeLoc, TaxonName taxonName){ |
|
195 |
Reference citation = null; |
|
196 |
String citationMicroReference = null; |
|
197 |
String originalNameString = null; |
|
198 |
boolean isNotDesignated = true; |
|
199 |
boolean addToAllHomotypicNames = true; |
|
200 |
|
|
201 |
SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance(); |
|
202 |
//elType |
|
203 |
if (elType != null){ |
|
204 |
doElType(elType, simpleSpecimen, config); |
|
205 |
}//elType |
|
206 |
|
|
207 |
//typeLoc |
|
208 |
HashMap<DerivedUnit, SpecimenTypeDesignationStatus> typeLocMap = null; |
|
209 |
if (elTypeLoc != null){ |
|
210 |
typeLocMap = doElTypeLoc(elTypeLoc, simpleSpecimen, taxonName, config); |
|
211 |
} |
|
212 |
if (typeLocMap != null && typeLocMap.size() >0){ |
|
213 |
for (DerivedUnit specimen : typeLocMap.keySet()){ |
|
214 |
SpecimenTypeDesignationStatus status = typeLocMap.get(specimen); |
|
215 |
taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames); |
|
216 |
} |
|
217 |
}else{ // no type_loc |
|
218 |
SpecimenTypeDesignationStatus status = null; |
|
219 |
taxonName.addSpecimenTypeDesignation(simpleSpecimen.getSpecimen(), status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames); |
|
220 |
} |
|
221 |
return true; |
|
222 |
} |
|
223 |
|
|
224 |
private boolean doElType(Element elType, SimpleSpecimen simpleSpecimen, TaxonXImportConfigurator config){ |
|
225 |
//type |
|
226 |
String text = elType.getTextNormalize(); |
|
227 |
if (text.endsWith(";")){ |
|
228 |
text = text + " "; |
|
229 |
} |
|
230 |
String[] type = text.split(";"); |
|
231 |
if (type.length != 3 ){ |
|
232 |
if (text.equals("")){ |
|
233 |
logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config)); |
|
234 |
}else{ |
|
235 |
logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config)); |
|
236 |
} |
|
237 |
simpleSpecimen.setTitleCache(elType.getTextNormalize()); |
|
238 |
}else{ |
|
239 |
String strLocality = type[0].trim(); |
|
240 |
if (! "".equals(strLocality)){ |
|
241 |
// simpleSpecimen.setLocality(strLocality); |
|
242 |
} |
|
243 |
|
|
244 |
String strCollector = type[1].trim(); |
|
245 |
if (! "".equals(strCollector)){ |
|
246 |
AgentBase collector = Person.NewTitledInstance(strCollector); |
|
247 |
// simpleSpecimen.setCollector(collector); |
|
248 |
} |
|
249 |
|
|
250 |
String strCollectorNumber = type[2].trim(); |
|
251 |
if (! "".equals(strCollectorNumber)){ |
|
252 |
// simpleSpecimen.setCollectorsNumber(strCollectorNumber); |
|
253 |
} |
|
254 |
|
|
255 |
String title = CdmUtils.concat(" ", new String[]{strLocality, strCollector, strCollectorNumber}); |
|
256 |
simpleSpecimen.setTitleCache(title); |
|
257 |
} |
|
258 |
return true; |
|
259 |
} |
|
260 |
|
|
261 |
private boolean doNameType(Element elType, TaxonName taxonName, TaxonXImportConfigurator config){ |
|
262 |
boolean success = true; |
|
263 |
//type |
|
264 |
String text = elType.getTextNormalize(); |
|
265 |
logger.info("Type: " + text); |
|
266 |
if (text.endsWith(";")){ |
|
267 |
text = text + " "; |
|
268 |
} |
|
269 |
String[] type = text.split(";"); |
|
270 |
if (type.length != 3 ){ |
|
271 |
if (text.equals("")){ |
|
272 |
logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config)); |
|
273 |
}else{ |
|
274 |
logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config)); |
|
275 |
} |
|
276 |
success = false; |
|
277 |
}else{ |
|
278 |
String statusStr = type[0].trim(); |
|
279 |
String taxonNameStr = type[1].trim(); |
|
280 |
String authorStr = type[2].trim(); |
|
281 |
NameTypeDesignationStatus status = getNameTypeStatus(statusStr); |
|
282 |
/*boolean isLectoType = getIsLectoType(statusStr);*/ |
|
283 |
|
|
284 |
// if (status == null){ |
|
285 |
// logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config)); |
|
286 |
// success = false; |
|
287 |
// }else{ |
|
288 |
// TaxonName childType = getChildrenNameType(taxonName, taxonNameStr, authorStr); |
|
289 |
// if (childType != null){ |
|
290 |
// return doNameTypeDesignation(taxonName, childType, status); |
|
291 |
// }else{ |
|
292 |
String[] epis = taxonNameStr.split(" "); |
|
293 |
String uninomial = epis[0].trim(); |
|
294 |
String specEpi = epis[1].trim(); |
|
295 |
|
|
296 |
Pager<TaxonName> nameTypes = getNameService().searchNames(uninomial, null, specEpi, null, Rank.SPECIES(), null, null, null, null); |
|
297 |
|
|
298 |
List<INonViralName> result = new ArrayList<>(); |
|
299 |
for (TaxonName nt : nameTypes.getRecords()){ |
|
300 |
if (compareAuthorship(nt, authorStr)){ |
|
301 |
result.add(nt); |
|
302 |
success &= doNameTypeDesignation(taxonName, nt, status/*, isLectoType*/); |
|
303 |
}else{ |
|
304 |
//TODO ? |
|
305 |
} |
|
306 |
} |
|
307 |
if (result.size() > 1){ |
|
308 |
logger.warn("More than 1 name matches: " + text); |
|
309 |
success = false; |
|
310 |
}else if (result.size() == 0){ |
|
311 |
logger.warn("No name matches: " + text + "(" + config.getSourceNameString() + ")"); |
|
312 |
success = false; |
|
313 |
} |
|
314 |
// } |
|
315 |
// } |
|
316 |
} |
|
317 |
return success; |
|
318 |
} |
|
319 |
|
|
320 |
|
|
321 |
// private TaxonName getChildrenNameType(TaxonName name, String typeStr, String authorStr){ |
|
322 |
// TaxonName result = null; |
|
323 |
// Set<TaxonBase> list = name.getTaxonBases(); |
|
324 |
// for (TaxonBase taxonBase : list){ |
|
325 |
// Taxon taxon; |
|
326 |
// if (taxonBase.isInstanceOf(Taxon.class)){ |
|
327 |
// taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
328 |
// }else{ |
|
329 |
// Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
330 |
// taxon = syn.getAcceptedTaxa().iterator().next(); |
|
331 |
// } |
|
332 |
// Set<Taxon> children = taxon.getTaxonomicChildren(); |
|
333 |
// for (Taxon child: children){ |
|
334 |
// INonViralName childName = child.getName(); |
|
335 |
// if (childName.getNameCache().equals(typeStr)){ |
|
336 |
// if (compareAuthorship(childName, authorStr)){ |
|
337 |
// return childName; |
|
338 |
// } |
|
339 |
// } |
|
340 |
// } |
|
341 |
// } |
|
342 |
// return result; |
|
343 |
// } |
|
344 |
|
|
345 |
private boolean compareAuthorship(INonViralName typeName, String authorStr){ |
|
346 |
boolean result = false; |
|
347 |
authorStr = authorStr.replaceAll("\\s+and\\s+", "&"); |
|
348 |
authorStr = authorStr.replaceAll("\\s*", ""); |
|
349 |
authorStr = authorStr.replaceAll("\\.$", ""); |
|
350 |
String typeCache = typeName.getAuthorshipCache().replaceAll("\\s*", ""); |
|
351 |
typeCache = typeCache.replaceAll("\\.$", ""); |
|
352 |
if (authorStr.equals(typeCache)){ |
|
353 |
return true; |
|
354 |
}else{ |
|
355 |
logger.info(" Authors different: " + authorStr + " <-> " + typeCache); |
|
356 |
} |
|
357 |
return result; |
|
358 |
} |
|
359 |
|
|
360 |
private NameTypeDesignationStatus getNameTypeStatus(String statusString){ |
|
361 |
//FIXME some types (not further defined types) do not exist yet |
|
362 |
if (true){ |
|
363 |
return null; |
|
364 |
} |
|
365 |
if (statusString.trim().equalsIgnoreCase("Type")){ |
|
366 |
return NameTypeDesignationStatus.ORIGINAL_DESIGNATION(); |
|
367 |
}else if (statusString.trim().equalsIgnoreCase("Lectotype")){ |
|
368 |
return NameTypeDesignationStatus.LECTOTYPE(); |
|
369 |
}else if (statusString.trim().equalsIgnoreCase("Holotype")){ |
|
370 |
logger.warn("Holotype does not yet exist in CDM"); |
|
371 |
return NameTypeDesignationStatus.NOT_APPLICABLE(); |
|
372 |
}else if (statusString.trim().equalsIgnoreCase("paratype")){ |
|
373 |
logger.warn("paratype does not yet exist in CDM"); |
|
374 |
return NameTypeDesignationStatus.NOT_APPLICABLE(); |
|
375 |
} |
|
376 |
else{ |
|
377 |
logger.warn("Status not recognized: " + statusString); |
|
378 |
return null; |
|
379 |
} |
|
380 |
} |
|
381 |
|
|
382 |
private boolean getIsLectoType(String statusString){ |
|
383 |
//FIXME may be deleted once getNameTypeStatus works finde |
|
384 |
if (statusString.trim().equals("Lectotype")){ |
|
385 |
return true; |
|
386 |
}else{ |
|
387 |
return false; |
|
388 |
} |
|
389 |
} |
|
390 |
|
|
391 |
|
|
392 |
private boolean doNameTypeDesignation(TaxonName name, TaxonName type, NameTypeDesignationStatus status/*, boolean isLectoType*/){ |
|
393 |
Reference citation = null; |
|
394 |
String citationMicroReference = null; |
|
395 |
String originalNameString = null; |
|
396 |
boolean addToAllHomotypicNames = true; |
|
397 |
|
|
398 |
// name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString, status, addToAllHomotypicNames); |
|
399 |
name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString,status, false, false, /*isLectoType, */false, addToAllHomotypicNames); |
|
400 |
return true; |
|
401 |
} |
|
402 |
|
|
403 |
/** |
|
404 |
* Reads the typeLoc element split in parts for eacht type (holo, iso,...) |
|
405 |
* @param elTypeLoc |
|
406 |
* @param simpleSpecimen |
|
407 |
* @param taxonName |
|
408 |
* @param config |
|
409 |
* @return |
|
410 |
*/ |
|
411 |
private HashMap<DerivedUnit, SpecimenTypeDesignationStatus> doElTypeLoc(Element elTypeLoc, |
|
412 |
SimpleSpecimen simpleSpecimen, |
|
413 |
TaxonName taxonName, |
|
414 |
TaxonXImportConfigurator config){ |
|
415 |
|
|
416 |
HashMap<DerivedUnit, SpecimenTypeDesignationStatus> result = new HashMap<DerivedUnit, SpecimenTypeDesignationStatus>(); |
|
417 |
|
|
418 |
String typeLocFullString = elTypeLoc.getTextTrim(); |
|
419 |
typeLocFullString = typeLocFullString.replace("(", "").replace(")", ""); |
|
420 |
String[] typeLocStatusList = typeLocFullString.split(";"); |
|
421 |
|
|
422 |
DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen(); |
|
423 |
|
|
424 |
|
|
425 |
for (String typeLocStatus : typeLocStatusList){ |
|
426 |
typeLocStatus = typeLocStatus.trim(); |
|
427 |
int pos = typeLocStatus.indexOf(" "); |
|
428 |
if (pos == -1){ |
|
429 |
logger.warn("Unknown format or empty type_loc : '" +typeLocStatus + "'" + getBracketSourceName(config)); |
|
430 |
result.put(originalSpecimen, null); |
|
431 |
}else{ |
|
432 |
String statusString = typeLocStatus.substring(0,pos); |
|
433 |
SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config); |
|
434 |
//TODO |
|
435 |
//String[] collectionStrings = typeLocStatus.substring(pos).split(","); |
|
436 |
String tmpCollString = typeLocStatus.substring(pos).trim(); |
|
437 |
//for(String collectionString : collectionStrings){ |
|
438 |
if (tmpCollString.contains("typ")){ |
|
439 |
logger.warn("Is this really only a collection string? : " + tmpCollString + getBracketSourceName(config)); |
|
440 |
} |
|
441 |
DerivedUnit specimen; |
|
442 |
specimen = (DerivedUnit)originalSpecimen.clone(); |
|
443 |
String title = originalSpecimen.getTitleCache(); |
|
444 |
title = title + "(" + tmpCollString + ")"; |
|
445 |
specimen.setTitleCache(title, true ); |
|
446 |
result.put(specimen, status); |
|
447 |
//} |
|
448 |
} |
|
449 |
} |
|
450 |
|
|
451 |
return result; |
|
452 |
} |
|
453 |
|
|
454 |
/** |
|
455 |
* |
|
456 |
* Reads the collection_event tag, creates the according data and stores it. |
|
457 |
* TODO under work |
|
458 |
* @param elNomenclature |
|
459 |
* @param nsTaxonx |
|
460 |
* @param taxonBase |
|
461 |
* @return |
|
462 |
*/ |
|
463 |
private boolean doCollectionEvent(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonBase taxonBase){ |
|
464 |
boolean result = false; |
|
465 |
if (elNomenclature == null){ |
|
466 |
return false; |
|
467 |
} |
|
468 |
Element elCollectionEvent = elNomenclature.getChild("collection_event", nsTaxonx); |
|
469 |
if (elCollectionEvent == null){ |
|
470 |
return result; |
|
471 |
} |
|
472 |
Element elLocality = elCollectionEvent.getChild("locality", nsTaxonx); |
|
473 |
Element elType = elCollectionEvent.getChild("type", nsTaxonx); |
|
474 |
Element elTypeLoc = elCollectionEvent.getChild("type_loc", nsTaxonx); |
|
475 |
|
|
476 |
//locality |
|
477 |
SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance(); |
|
478 |
String locality = elLocality.getTextNormalize(); |
|
479 |
if (! "".equals(locality)){ |
|
480 |
simpleSpecimen.setLocality(locality); |
|
481 |
} |
|
482 |
|
|
483 |
//type |
|
484 |
String[] type = elType.getTextNormalize().split(" "); |
|
485 |
if (type.length != 2 ){ |
|
486 |
logger.warn("<collecion_even><type> is of unsupported format: " + elType.getTextNormalize()); |
|
487 |
}else{ |
|
488 |
AgentBase collector = Person.NewTitledInstance(type[0]); |
|
489 |
simpleSpecimen.setCollector(collector); |
|
490 |
|
|
491 |
String collectorNumber = type[1]; |
|
492 |
simpleSpecimen.setCollectorsNumber(collectorNumber); |
|
493 |
} |
|
494 |
|
|
495 |
//typeLoc |
|
496 |
String typeLocFullString = elTypeLoc.getTextTrim(); |
|
497 |
typeLocFullString = typeLocFullString.replace("(", "").replace(")", ""); |
|
498 |
String[] typeLocStatusList = typeLocFullString.split(";"); |
|
499 |
|
|
500 |
DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen(); |
|
501 |
|
|
502 |
//TODO special character ?, �, ! |
|
503 |
|
|
504 |
for (String typeLocStatus : typeLocStatusList){ |
|
505 |
typeLocStatus = typeLocStatus.trim(); |
|
506 |
int pos = typeLocStatus.indexOf(" "); |
|
507 |
if (pos == -1){ |
|
508 |
logger.warn("Unknown format: " + typeLocStatus); |
|
509 |
}else{ |
|
510 |
String statusString = typeLocStatus.substring(0,pos); |
|
511 |
SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config); |
|
512 |
String[] collectionStrings = typeLocStatus.substring(pos).split(","); |
|
513 |
for(String collectionString : collectionStrings){ |
|
514 |
if (taxonBase != null){ |
|
515 |
TaxonName taxonName = taxonBase.getName(); |
|
516 |
if (taxonName != null){ |
|
517 |
Reference citation = null; |
|
518 |
String citationMicroReference = null; |
|
519 |
String originalNameString = null; |
|
520 |
boolean isNotDesignated = true; |
|
521 |
boolean addToAllHomotypicNames = true; |
|
522 |
DerivedUnit specimen = (DerivedUnit)originalSpecimen.clone(); |
|
523 |
unlazyTypeDesignation(config, taxonName); |
|
524 |
taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames); |
|
525 |
result = true; |
|
526 |
} |
|
527 |
} |
|
528 |
} |
|
529 |
} |
|
530 |
} |
|
531 |
return result; |
|
532 |
} |
|
533 |
|
|
534 |
|
|
535 |
private static Map<String, SpecimenTypeDesignationStatus> statusMap; |
|
536 |
private static void fillTypeStatusMap(){ |
|
537 |
statusMap = new HashMap<String, SpecimenTypeDesignationStatus>(); |
|
538 |
statusMap.put("epitype", SpecimenTypeDesignationStatus.EPITYPE()); |
|
539 |
statusMap.put("holotype", SpecimenTypeDesignationStatus.HOLOTYPE()); |
|
540 |
statusMap.put("iconotype", SpecimenTypeDesignationStatus.ICONOTYPE()); |
|
541 |
statusMap.put("isotype", SpecimenTypeDesignationStatus.ISOTYPE()); |
|
542 |
statusMap.put("isoneotype", SpecimenTypeDesignationStatus.ISONEOTYPE()); |
|
543 |
statusMap.put("isosyntype", SpecimenTypeDesignationStatus.ISOSYNTYPE()); |
|
544 |
statusMap.put("isolectotype", SpecimenTypeDesignationStatus.ISOLECTOTYPE()); |
|
545 |
statusMap.put("lectotype", SpecimenTypeDesignationStatus.LECTOTYPE()); |
|
546 |
statusMap.put("syntype", SpecimenTypeDesignationStatus.SYNTYPE()); |
|
547 |
statusMap.put("paratype", SpecimenTypeDesignationStatus.PARATYPE()); |
|
548 |
statusMap.put("neotype", SpecimenTypeDesignationStatus.NEOTYPE()); |
|
549 |
statusMap.put("isoepitype", SpecimenTypeDesignationStatus.ISOEPITYPE()); |
|
550 |
statusMap.put("originalmaterial", SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL()); |
|
551 |
statusMap.put("paralectotype", SpecimenTypeDesignationStatus.PARALECTOTYPE()); |
|
552 |
statusMap.put("paraneotype", SpecimenTypeDesignationStatus.PARANEOTYPE()); |
|
553 |
statusMap.put("phototype", SpecimenTypeDesignationStatus.PHOTOTYPE()); |
|
554 |
statusMap.put("secondsteplectotype", SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE()); |
|
555 |
statusMap.put("secondstepneotype", SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE()); |
|
556 |
statusMap.put("type", null); |
|
557 |
} |
|
558 |
|
|
559 |
|
|
560 |
//TODO move to TypeDesignation class |
|
561 |
/** |
|
562 |
* Returns the typeDesignationStatus according to a type designation status string |
|
563 |
* @param statusString |
|
564 |
* @return TypeDesignationStatus |
|
565 |
*/ |
|
566 |
private static SpecimenTypeDesignationStatus getStatusByStatusString(String statusString, TaxonXImportConfigurator config){ |
|
567 |
SpecimenTypeDesignationStatus result = null; |
|
568 |
if (statusString == null || "".equals(statusString.trim())){ |
|
569 |
return null; |
|
570 |
} |
|
571 |
statusString = statusString.trim().toLowerCase(); |
|
572 |
statusString = statusString.replace("typi", "typus"); |
|
573 |
statusString = statusString.replace("typus", "type"); |
|
574 |
statusString = statusString.replace("types", "type"); |
|
575 |
statusString = statusString.toLowerCase(); |
|
576 |
|
|
577 |
if (statusMap == null){ |
|
578 |
fillTypeStatusMap(); |
|
579 |
} |
|
580 |
result = statusMap.get(statusString); |
|
581 |
if (statusString.equals("type")){ |
|
582 |
logger.info("No type designation type" + getBracketSourceName(config)); |
|
583 |
}else if (result == null){ |
|
584 |
logger.warn("Unknown type status string: " + statusString + getBracketSourceName(config)); |
|
585 |
} |
|
586 |
return result; |
|
587 |
} |
|
588 |
|
|
589 |
|
|
590 |
/** |
|
591 |
* TODO Preliminary to avoid laizy loading errors |
|
592 |
*/ |
|
593 |
private void unlazyTypeDesignation(TaxonXImportConfigurator config, TaxonName taxonName){ |
|
594 |
TransactionStatus txStatus = startTransaction(); |
|
595 |
//INameService taxonNameService = config.getCdmAppController().getNameService(); |
|
596 |
INameService taxonNameService = getNameService(); |
|
597 |
|
|
598 |
taxonNameService.save(taxonName); |
|
599 |
Set<TaxonName> typifiedNames = taxonName.getHomotypicalGroup().getTypifiedNames(); |
|
600 |
for(TaxonName typifiedName: typifiedNames){ |
|
601 |
typifiedName.getTypeDesignations().size(); |
|
602 |
} |
|
603 |
//taxonNameService.saveTaxonName(taxonName); |
|
604 |
commitTransaction(txStatus); |
|
605 |
} |
|
606 |
|
|
607 |
/** |
|
608 |
* TODO Preliminary to avoid laizy loading errors |
|
609 |
*/ |
|
610 |
private void unlazySynonym(IImportConfigurator config, Taxon taxon){ |
|
611 |
TransactionStatus txStatus = startTransaction(); |
|
612 |
ITaxonService taxonService = getTaxonService(); |
|
613 |
taxonService.save(taxon); |
|
614 |
Set<Synonym> synonyms = taxon.getSynonyms(); |
|
615 |
logger.debug(synonyms.size()); |
|
616 |
//taxonService.saveTaxon(taxon); |
|
617 |
commitTransaction(txStatus); |
|
618 |
} |
|
619 |
|
|
620 |
private static String getBracketSourceName(TaxonXImportConfigurator config){ |
|
621 |
return "(" + config.getSourceNameString() + ")"; |
|
622 |
} |
|
623 |
|
|
624 |
|
|
625 |
} |
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