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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.specimen.abcd206.in;
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import java.io.ByteArrayOutputStream;
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import java.io.PrintStream;
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import java.net.MalformedURLException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.w3c.dom.Element;
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import org.w3c.dom.NodeList;
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
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import eu.etaxonomy.cdm.io.specimen.SpecimenUserInteraction;
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import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
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import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular.AbcdDnaParser;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.name.BacterialName;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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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.SpecimenTypeDesignation;
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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.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
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/**
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* @author p.kelbert
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* @author pplitzner
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* @created 20.10.2008
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*/
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@Component
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public class Abcd206Import extends SpecimenImportBase<Abcd206ImportConfigurator, Abcd206ImportState> {
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private static final Logger logger = Logger.getLogger(Abcd206Import.class);
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private final boolean DEBUG = true;
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private static final String COLON = ":";
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private Abcd206ImportReport report;
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public Abcd206Import() {
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super();
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}
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@Override
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protected boolean doCheck(Abcd206ImportState state) {
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logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
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return true;
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}
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@Override
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@SuppressWarnings("rawtypes")
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public void doInvoke(Abcd206ImportState state) {
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report = new Abcd206ImportReport();
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try{
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state.setTx(startTransaction());
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logger.info("INVOKE Specimen Import from ABCD2.06 XML ");
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//init cd repository
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if(state.getCdmRepository()==null){
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state.setCdmRepository(this);
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}
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SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
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//init import reference
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List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
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if (state.getConfig().isInteractWithUser()){
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Map<String,Reference> refMap = new HashMap<String, Reference>();
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for (Reference reference : references) {
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if (! StringUtils.isBlank(reference.getTitleCache())) {
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refMap.put(reference.getTitleCache(),reference);
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}
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}
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state.setRef(sui.askForReference(refMap));
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if (state.getRef() == null){
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String cla = sui.createNewReference();
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if (refMap.get(cla)!= null) {
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state.setRef(refMap.get(cla));
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} else {
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state.setRef(ReferenceFactory.newGeneric());
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state.getRef().setTitle(cla);
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}
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}
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else{
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state.setRef(getReferenceService().find(state.getRef().getUuid()));
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}
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}else{
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if (state.getRef()==null){
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String name = NB(state.getConfig().getSourceReferenceTitle());
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for (Reference reference : references) {
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if (! StringUtils.isBlank(reference.getTitleCache())) {
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if (reference.getTitleCache().equalsIgnoreCase(name)) {
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state.setRef(reference);
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}
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}
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}
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if (state.getRef() == null){
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state.setRef(ReferenceFactory.newGeneric());
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state.getRef().setTitle("ABCD classic");
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}
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}
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}
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save(state.getRef(), state);
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state.getConfig().setSourceReference(state.getRef());
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if(state.getConfig().getClassificationUuid()!=null){
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//load classification from config if it exists
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state.setClassification(getClassificationService().load(state.getConfig().getClassificationUuid()));
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}
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if(state.getClassification()==null){//no existing classification was set in config
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List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, null);
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//get classification via user interaction
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if (state.getConfig().isUseClassification() && state.getConfig().isInteractWithUser()){
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Map<String,Classification> classMap = new HashMap<String, Classification>();
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for (Classification tree : classificationList) {
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if (! StringUtils.isBlank(tree.getTitleCache())) {
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classMap.put(tree.getTitleCache(),tree);
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}
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}
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state.setClassification(sui.askForClassification(classMap));
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if (state.getClassification() == null){
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String cla = sui.createNewClassification();
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if (classMap.get(cla)!= null) {
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state.setClassification(classMap.get(cla));
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} else {
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state.setClassification(Classification.NewInstance(cla, state.getRef(), Language.DEFAULT()));
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}
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}
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save(state.getClassification(), state);
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}
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// use default classification as the classification to import into
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if (state.getClassification() == null) {
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String name = NB(state.getConfig().getClassificationName());
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for (Classification classif : classificationList){
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if (classif.getTitleCache() != null && classif.getCitation() != null
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&& classif.getTitleCache().equalsIgnoreCase(name) && classif.getCitation().equals(state.getRef())) {
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state.setClassification(classif);
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}
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}
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if (state.getClassification() == null){
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state.setClassification(Classification.NewInstance(name, state.getRef(), Language.DEFAULT()));
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//we do not need a default classification when creating an empty new one
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state.setDefaultClassification(state.getClassification());
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save(state.getDefaultClassification(), state);
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}
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save(state.getClassification(), state);
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}
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}
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UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(state.getConfig().getSource(), report);
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NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();
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state.setPrefix(unitAssociationWrapper.getPrefix());
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if (unitsList != null) {
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String message = "nb units to insert: " + unitsList.getLength();
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logger.info(message);
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state.getConfig().getProgressMonitor().beginTask("Importing ABCD file", unitsList.getLength() + 2);
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updateProgress(state, message);
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state.setDataHolder(new Abcd206DataHolder());
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state.getDataHolder().reset();
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Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix());
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prepareCollectors(state, unitsList, abcdFieldGetter);
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state.setAssociationRefs(new ArrayList<OriginalSourceBase<?>>());
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state.setDescriptionRefs(new ArrayList<OriginalSourceBase<?>>());
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state.setDerivedUnitSources(new ArrayList<OriginalSourceBase<?>>());
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for (int i = 0; i < unitsList.getLength(); i++) {
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if(state.getConfig().getProgressMonitor().isCanceled()){
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break;
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}
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state.reset();
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Element item = (Element) unitsList.item(i);
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this.setUnitPropertiesXML( item, abcdFieldGetter, state);
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updateProgress(state, "Importing data for unit "+state.getDataHolder().unitID+" ("+i+"/"+unitsList.getLength()+")");
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//import unit + field unit data
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this.handleSingleUnit(state, item);
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}
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if(state.getConfig().isDeduplicateReferences()){
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getReferenceService().deduplicate(Reference.class, null, null);
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}
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if(state.getConfig().isDeduplicateClassifications()){
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getClassificationService().deduplicate(Classification.class, null, null);
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}
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}
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commitTransaction(state.getTx());
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}
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catch(Exception e){
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String errorDuringImport = "Exception during import!";
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logger.error(errorDuringImport, e);
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report.addException(errorDuringImport, e);
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}
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finally{
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report.printReport(state.getConfig().getReportUri());
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}
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return;
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}
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/**
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* Handle a single unit
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* @param state
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* @param item
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*/
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@SuppressWarnings("rawtypes")
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private void handleSingleUnit(Abcd206ImportState state, Element item) {
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if (DEBUG) {
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logger.info("handleSingleUnit "+state.getRef());
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}
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try {
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ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
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if(cdmAppController==null){
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cdmAppController = this;
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}
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//check if unit already exists
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DerivedUnitFacade derivedUnitFacade = null;
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if(state.getConfig().isIgnoreImportOfExistingSpecimens()){
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SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(state.getDataHolder().unitID, state);
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if(existingSpecimen!=null && existingSpecimen.isInstanceOf(DerivedUnit.class)){
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DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);
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state.setDerivedUnitBase(derivedUnit);
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derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
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importAssociatedUnits(state, item, derivedUnitFacade);
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report.addAlreadyExistingSpecimen(AbcdImportUtility.getUnitID(derivedUnit, state.getConfig()), derivedUnit);
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return;
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}
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}
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// TODO: implement overwrite/merge specimen
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// else if(state.getConfig().isOverwriteExistingSpecimens()){
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// Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
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// if(!existingSpecimens.getRecords().isEmpty()){
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// derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit);
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// derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
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// fieldUnit = derivedUnitFacade.getFieldUnit(true);
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// }
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// }
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//import new specimen
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// import DNA unit
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if(state.getDataHolder().kindOfUnit!=null && state.getDataHolder().kindOfUnit.equalsIgnoreCase("dna")){
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AbcdDnaParser dnaParser = new AbcdDnaParser(state.getPrefix(), report, state.getCdmRepository());
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DnaSample dnaSample = dnaParser.parse(item, state);
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save(dnaSample, state);
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//set dna as derived unit to avoid creating an extra specimen for this dna sample (instead just the field unit will be created)
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state.setDerivedUnitBase(dnaSample);
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derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
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}
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else{
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// create facade
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derivedUnitFacade = getFacade(state);
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state.setDerivedUnitBase(derivedUnitFacade.innerDerivedUnit());
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}
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/**
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* GATHERING EVENT
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*/
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// gathering event
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334
|
UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(cdmAppController.getTermService(),
|
|
335
|
state.getDataHolder().locality, state.getDataHolder().languageIso, state.getDataHolder().longitude, state.getDataHolder().latitude,
|
|
336
|
state.getDataHolder().gatheringElevationText, state.getDataHolder().gatheringElevationMin,
|
|
337
|
state.getDataHolder().gatheringElevationMax, state.getDataHolder().gatheringElevationUnit, state.getDataHolder().gatheringDateText,
|
|
338
|
state.getDataHolder().gatheringAgentList, state.getDataHolder().gatheringTeamList, state.getConfig());
|
|
339
|
|
|
340
|
// country
|
|
341
|
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
|
|
342
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());
|
|
343
|
unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, state.getConfig(), cdmAppController.getTermService(), cdmAppController.getOccurrenceService());
|
|
344
|
|
|
345
|
DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();
|
|
346
|
|
|
347
|
// other areas
|
|
348
|
unitsGatheringArea = new UnitsGatheringArea();
|
|
349
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());
|
|
350
|
unitsGatheringArea.setAreas(state.getDataHolder().namedAreaList,state.getConfig(), cdmAppController.getTermService(), cdmAppController.getVocabularyService());
|
|
351
|
ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
|
|
352
|
for (DefinedTermBase namedArea : nas) {
|
|
353
|
unitsGatheringEvent.addArea(namedArea);
|
|
354
|
}
|
|
355
|
|
|
356
|
// copy gathering event to facade
|
|
357
|
GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
|
|
358
|
derivedUnitFacade.setLocality(gatheringEvent.getLocality());
|
|
359
|
derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
|
|
360
|
derivedUnitFacade.setCollector(gatheringEvent.getCollector());
|
|
361
|
derivedUnitFacade.setCountry((NamedArea)areaCountry);
|
|
362
|
derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());
|
|
363
|
derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());
|
|
364
|
derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());
|
|
365
|
derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
|
|
366
|
|
|
367
|
for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
|
|
368
|
derivedUnitFacade.addCollectingArea((NamedArea) area);
|
|
369
|
}
|
|
370
|
// derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
|
|
371
|
// TODO exsiccatum
|
|
372
|
|
|
373
|
// add fieldNumber
|
|
374
|
derivedUnitFacade.setFieldNumber(NB(state.getDataHolder().fieldNumber));
|
|
375
|
|
|
376
|
// //add Multimedia URLs
|
|
377
|
if (state.getDataHolder().multimediaObjects.size() != -1) {
|
|
378
|
for (String multimediaObject : state.getDataHolder().multimediaObjects) {
|
|
379
|
Media media;
|
|
380
|
try {
|
|
381
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
382
|
derivedUnitFacade.addDerivedUnitMedia(media);
|
|
383
|
if(state.getConfig().isAddMediaAsMediaSpecimen()){
|
|
384
|
//add media also as specimen scan
|
|
385
|
MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.Media);
|
|
386
|
mediaSpecimen.setMediaSpecimen(media);
|
|
387
|
DefinedTermBase specimenScanTerm = getTermService().load(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"));
|
|
388
|
if(specimenScanTerm instanceof DefinedTerm){
|
|
389
|
mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
|
|
390
|
}
|
|
391
|
DerivationEvent derivationEvent = DerivationEvent.NewInstance(DerivationEventType.PREPARATION());
|
|
392
|
derivationEvent.addDerivative(mediaSpecimen);
|
|
393
|
derivedUnitFacade.innerDerivedUnit().addDerivationEvent(derivationEvent);
|
|
394
|
}
|
|
395
|
|
|
396
|
} catch (MalformedURLException e) {
|
|
397
|
// TODO Auto-generated catch block
|
|
398
|
e.printStackTrace();
|
|
399
|
}
|
|
400
|
|
|
401
|
}
|
|
402
|
}
|
|
403
|
|
|
404
|
// /*
|
|
405
|
// * merge AND STORE DATA
|
|
406
|
// */
|
|
407
|
// getTermService().saveOrUpdate(areaCountry);// TODO save area sooner
|
|
408
|
//
|
|
409
|
// for (NamedArea area : otherAreas) {
|
|
410
|
// getTermService().saveOrUpdate(area);// merge it sooner (foreach area)
|
|
411
|
// }
|
|
412
|
|
|
413
|
save(unitsGatheringEvent.getLocality(), state);
|
|
414
|
|
|
415
|
// handle collection data
|
|
416
|
setCollectionData(state, derivedUnitFacade);
|
|
417
|
|
|
418
|
//Reference stuff
|
|
419
|
SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
|
|
420
|
Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
|
|
421
|
|
|
422
|
state.getDataHolder().docSources = new ArrayList<String>();
|
|
423
|
for (String[] fullReference : state.getDataHolder().referenceList) {
|
|
424
|
String strReference=fullReference[0];
|
|
425
|
String citationDetail = fullReference[1];
|
|
426
|
String citationURL = fullReference[2];
|
|
427
|
|
|
428
|
if (!citationURL.isEmpty()) {
|
|
429
|
citationDetail+=", "+citationURL;
|
|
430
|
}
|
|
431
|
|
|
432
|
Reference<?> reference;
|
|
433
|
if(strReference.equals(state.getRef().getTitleCache())){
|
|
434
|
reference = state.getRef();
|
|
435
|
}
|
|
436
|
else{
|
|
437
|
reference = ReferenceFactory.newGeneric();
|
|
438
|
reference.setTitle(strReference);
|
|
439
|
}
|
|
440
|
|
|
441
|
IdentifiableSource sour = getIdentifiableSource(reference,citationDetail);
|
|
442
|
|
|
443
|
try{
|
|
444
|
if (sour.getCitation() != null){
|
|
445
|
if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {
|
|
446
|
state.getDataHolder().docSources.add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());
|
|
447
|
} else {
|
|
448
|
state.getDataHolder().docSources.add(sour.getCitation().getTitleCache());
|
|
449
|
}
|
|
450
|
}
|
|
451
|
}catch(Exception e){
|
|
452
|
logger.warn("oups");
|
|
453
|
}
|
|
454
|
reference.addSource(sour);
|
|
455
|
save(reference, state);
|
|
456
|
}
|
|
457
|
|
|
458
|
List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
459
|
List<DescriptionElementSource> issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
460
|
|
|
461
|
Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
|
|
462
|
if(issTmp2!=null) {
|
|
463
|
osbSet.addAll(issTmp2);
|
|
464
|
}
|
|
465
|
if(issTmp!=null) {
|
|
466
|
osbSet.addAll(issTmp);
|
|
467
|
}
|
|
468
|
|
|
469
|
addToSourceMap(sourceMap, osbSet);
|
|
470
|
|
|
471
|
if( state.getConfig().isInteractWithUser()){
|
|
472
|
List<OriginalSourceBase<?>>sources=null;
|
|
473
|
if(!state.isDerivedUnitSourcesSet()){
|
|
474
|
sources= sui.askForSource(sourceMap, "the unit itself","",getReferenceService(), state.getDataHolder().docSources);
|
|
475
|
state.setDerivedUnitSources(sources);
|
|
476
|
state.setDerivedUnitSourcesSet(true);
|
|
477
|
}
|
|
478
|
else{
|
|
479
|
sources=state.getDerivedUnitSources();
|
|
480
|
}
|
|
481
|
// System.out.println("nb sources: "+sources.size());
|
|
482
|
// System.out.println("derivedunitfacade : "+derivedUnitFacade.getTitleCache());
|
|
483
|
for (OriginalSourceBase<?> sour:sources){
|
|
484
|
if(sour.isInstanceOf(IdentifiableSource.class)){
|
|
485
|
if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {
|
|
486
|
// System.out.println("add source to derivedunitfacade1 "+derivedUnitFacade.getTitleCache());
|
|
487
|
derivedUnitFacade.addSource((IdentifiableSource)sour.clone());
|
|
488
|
}
|
|
489
|
}else{
|
|
490
|
if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {
|
|
491
|
// System.out.println("add source to derivedunitfacade2 "+derivedUnitFacade.getTitleCache());
|
|
492
|
derivedUnitFacade.addSource(OriginalSourceType.Import,sour.getCitation(),sour.getCitationMicroReference(), ioName);
|
|
493
|
}
|
|
494
|
}
|
|
495
|
}
|
|
496
|
}else{
|
|
497
|
for (OriginalSourceBase<?> sr : sourceMap.values()){
|
|
498
|
if(sr.isInstanceOf(IdentifiableSource.class)){
|
|
499
|
if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
|
|
500
|
// System.out.println("add source to derivedunitfacade3 "+derivedUnitFacade.getTitleCache());
|
|
501
|
derivedUnitFacade.addSource((IdentifiableSource)sr.clone());
|
|
502
|
}
|
|
503
|
}else{
|
|
504
|
if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
|
|
505
|
// System.out.println("add source to derivedunitfacade4 "+derivedUnitFacade.getTitleCache());
|
|
506
|
derivedUnitFacade.addSource(OriginalSourceType.Import,sr.getCitation(),sr.getCitationMicroReference(), ioName);
|
|
507
|
}
|
|
508
|
}
|
|
509
|
}
|
|
510
|
}
|
|
511
|
|
|
512
|
save(state.getDerivedUnitBase(), state);
|
|
513
|
|
|
514
|
if(DEBUG) {
|
|
515
|
logger.info("saved ABCD specimen ...");
|
|
516
|
}
|
|
517
|
|
|
518
|
// handle identifications
|
|
519
|
handleIdentifications(state, derivedUnitFacade);
|
|
520
|
|
|
521
|
//associatedUnits
|
|
522
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
523
|
|
|
524
|
|
|
525
|
|
|
526
|
} catch (Exception e) {
|
|
527
|
String message = "Error when reading record!";
|
|
528
|
logger.warn(message);
|
|
529
|
report.addException(message, e);
|
|
530
|
e.printStackTrace();
|
|
531
|
state.setUnsuccessfull();
|
|
532
|
}
|
|
533
|
|
|
534
|
return;
|
|
535
|
}
|
|
536
|
|
|
537
|
private void importAssociatedUnits(Abcd206ImportState state, Element item, DerivedUnitFacade derivedUnitFacade) {
|
|
538
|
//import associated units
|
|
539
|
FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();
|
|
540
|
//TODO: push state (think of implementing stack architecture for state
|
|
541
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
542
|
DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
543
|
String currentPrefix = state.getPrefix();
|
|
544
|
NodeList unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");
|
|
545
|
for(int k=0;k<unitAssociationList.getLength();k++){
|
|
546
|
if(unitAssociationList.item(k) instanceof Element){
|
|
547
|
Element unitAssociation = (Element)unitAssociationList.item(k);
|
|
548
|
UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, report, state.getCdmRepository());
|
|
549
|
UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
|
|
550
|
if(associationWrapper!=null){
|
|
551
|
NodeList associatedUnits = associationWrapper.getAssociatedUnits();
|
|
552
|
for(int m=0;m<associatedUnits.getLength();m++){
|
|
553
|
if(associatedUnits.item(m) instanceof Element){
|
|
554
|
state.reset();
|
|
555
|
state.setPrefix(associationWrapper.getPrefix());
|
|
556
|
this.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
|
|
557
|
handleSingleUnit(state, (Element) associatedUnits.item(m));
|
|
558
|
|
|
559
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
560
|
FieldUnit associatedFieldUnit = null;
|
|
561
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());
|
|
562
|
//ignore field unit if associated unit has more than one
|
|
563
|
if(associatedFieldUnits.size()>1){
|
|
564
|
report.addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
565
|
}
|
|
566
|
else if(associatedFieldUnits.size()==1){
|
|
567
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
568
|
}
|
|
569
|
|
|
570
|
//attach current unit and associated unit depending on association type
|
|
571
|
|
|
572
|
//parent-child relation:
|
|
573
|
//copy derivation event and connect parent and sub derivative
|
|
574
|
if(associationWrapper.getAssociationType().contains("individual")){
|
|
575
|
if(currentDerivedFrom==null){
|
|
576
|
report.addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",AbcdImportUtility.getUnitID(currentUnit, state.getConfig())));
|
|
577
|
DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());
|
|
578
|
}
|
|
579
|
else{
|
|
580
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());
|
|
581
|
updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
582
|
updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
583
|
updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
584
|
updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
585
|
}
|
|
586
|
report.addDerivate(associatedUnit, currentUnit, state.getConfig());
|
|
587
|
}
|
|
588
|
//siblings relation
|
|
589
|
//connect current unit to field unit of associated unit
|
|
590
|
else if(associationWrapper.getAssociationType().contains("population")){
|
|
591
|
//no associated field unit -> using current one
|
|
592
|
if(associatedFieldUnit==null){
|
|
593
|
if(currentFieldUnit!=null){
|
|
594
|
DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());
|
|
595
|
}
|
|
596
|
}
|
|
597
|
else{
|
|
598
|
if(currentDerivedFrom==null){
|
|
599
|
report.addInfoMessage("No derivation event found for unit "+AbcdImportUtility.getUnitID(currentUnit, state.getConfig())+". Defaulting to ACCESIONING event.");
|
|
600
|
DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());
|
|
601
|
}
|
|
602
|
if(currentDerivedFrom!=null && associatedFieldUnit!=currentFieldUnit){
|
|
603
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());
|
|
604
|
updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
605
|
updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
606
|
updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
607
|
updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
608
|
}
|
|
609
|
}
|
|
610
|
}
|
|
611
|
|
|
612
|
//delete current field unit if replaced
|
|
613
|
if(currentFieldUnit!=null && currentDerivedFrom!=null
|
|
614
|
&& currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit
|
|
615
|
&& currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units
|
|
616
|
&& currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted
|
|
617
|
){
|
|
618
|
currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
|
|
619
|
state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);
|
|
620
|
}
|
|
621
|
|
|
622
|
save(associatedUnit, state);
|
|
623
|
}
|
|
624
|
}
|
|
625
|
}
|
|
626
|
}
|
|
627
|
}
|
|
628
|
//TODO: pop state
|
|
629
|
state.reset();
|
|
630
|
state.setDerivedUnitBase(currentUnit);
|
|
631
|
state.setPrefix(currentPrefix);
|
|
632
|
}
|
|
633
|
|
|
634
|
private SpecimenOrObservationBase findExistingSpecimen(String unitId, Abcd206ImportState state){
|
|
635
|
ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
|
|
636
|
if(cdmAppController==null){
|
|
637
|
cdmAppController = this;
|
|
638
|
}
|
|
639
|
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
|
|
640
|
config.setSignificantIdentifier(unitId);
|
|
641
|
Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
|
|
642
|
if(!existingSpecimens.getRecords().isEmpty()){
|
|
643
|
if(existingSpecimens.getRecords().size()==1){
|
|
644
|
return existingSpecimens.getRecords().iterator().next();
|
|
645
|
}
|
|
646
|
}
|
|
647
|
return null;
|
|
648
|
}
|
|
649
|
|
|
650
|
/**
|
|
651
|
* @param sourceMap
|
|
652
|
* @param osbSet
|
|
653
|
*/
|
|
654
|
private void addToSourceMap(Map<String, OriginalSourceBase<?>> sourceMap, Set<OriginalSourceBase> osbSet) {
|
|
655
|
for( OriginalSourceBase<?> osb:osbSet) {
|
|
656
|
if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
|
|
657
|
try{
|
|
658
|
sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
|
|
659
|
}catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
|
|
660
|
} else if(osb.getCitation()!=null){
|
|
661
|
try{
|
|
662
|
sourceMap.put(osb.getCitation().getTitleCache(),osb);
|
|
663
|
}catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
|
|
664
|
}
|
|
665
|
}
|
|
666
|
}
|
|
667
|
|
|
668
|
/**
|
|
669
|
* @param derivedUnitFacade
|
|
670
|
* @param sour
|
|
671
|
* @return
|
|
672
|
*/
|
|
673
|
private boolean sourceNotLinkedToElement(DerivedUnitFacade derivedUnitFacade, OriginalSourceBase<?> source) {
|
|
674
|
Set<IdentifiableSource> linkedSources = derivedUnitFacade.getSources();
|
|
675
|
for (IdentifiableSource is:linkedSources){
|
|
676
|
if (is.getCitation()!=null && source.getCitation()!=null &&
|
|
677
|
is.getCitation().getTitleCache().equalsIgnoreCase(source.getCitation().getTitleCache())){
|
|
678
|
String isDetail = is.getCitationMicroReference();
|
|
679
|
if ((StringUtils.isBlank(isDetail) && StringUtils.isBlank(source.getCitationMicroReference()))
|
|
680
|
|| (isDetail != null && isDetail.equalsIgnoreCase(source.getCitationMicroReference())) ) {
|
|
681
|
return false;
|
|
682
|
}
|
|
683
|
}
|
|
684
|
}
|
|
685
|
return true;
|
|
686
|
}
|
|
687
|
|
|
688
|
/**
|
|
689
|
* @param reference
|
|
690
|
* @param citationDetail
|
|
691
|
* @return
|
|
692
|
*/
|
|
693
|
//FIXME this method is highly critical, because
|
|
694
|
// * it will have serious performance and memory problems with large databases
|
|
695
|
// (databases may easily have >1 Mio source records)
|
|
696
|
// * it does not make sense to search for existing sources and then clone them
|
|
697
|
// we need to search for existing references instead and use them (if exist)
|
|
698
|
// for our new source.
|
|
699
|
private IdentifiableSource getIdentifiableSource(Reference<?> reference, String citationDetail) {
|
|
700
|
|
|
701
|
List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
702
|
|
|
703
|
|
|
704
|
if (reference != null){
|
|
705
|
try {
|
|
706
|
for (OriginalSourceBase<?> osb: issTmp){
|
|
707
|
if (osb.getCitation() != null && osb.getCitation().getTitleCache().equalsIgnoreCase(reference.getTitleCache())){
|
|
708
|
String osbDetail = osb.getCitationMicroReference();
|
|
709
|
if ((StringUtils.isBlank(osbDetail) && StringUtils.isBlank(citationDetail))
|
|
710
|
|| (osbDetail != null && osbDetail.equalsIgnoreCase(citationDetail)) ) {
|
|
711
|
// System.out.println("REFERENCE FOUND RETURN EXISTING SOURCE");
|
|
712
|
return (IdentifiableSource) osb.clone();
|
|
713
|
}
|
|
714
|
}
|
|
715
|
}
|
|
716
|
} catch (CloneNotSupportedException e) {
|
|
717
|
throw new RuntimeException(e);
|
|
718
|
} catch (Exception e1){
|
|
719
|
e1.printStackTrace();
|
|
720
|
}
|
|
721
|
}
|
|
722
|
|
|
723
|
IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
|
|
724
|
return sour;
|
|
725
|
}
|
|
726
|
|
|
727
|
// /**
|
|
728
|
// * @param reference
|
|
729
|
// * @param citationDetail
|
|
730
|
// * @return
|
|
731
|
// */
|
|
732
|
// private DescriptionElementSource getDescriptionSource(Reference<?> reference, String citationDetail) {
|
|
733
|
//
|
|
734
|
// List<OriginalSourceBase> issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
735
|
//
|
|
736
|
// try {
|
|
737
|
// for (OriginalSourceBase<?> osb:issTmp2){
|
|
738
|
// if (osb.getCitation().equals(reference) && osb.getCitationMicroReference().equalsIgnoreCase(citationDetail)) {
|
|
739
|
// return (DescriptionElementSource) osb.clone();
|
|
740
|
// }
|
|
741
|
// }
|
|
742
|
// } catch (CloneNotSupportedException e) {
|
|
743
|
// // TODO Auto-generated catch block
|
|
744
|
// e.printStackTrace();
|
|
745
|
// }
|
|
746
|
//
|
|
747
|
// DescriptionElementSource sour = DescriptionElementSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
|
|
748
|
// return sour;
|
|
749
|
// }
|
|
750
|
|
|
751
|
|
|
752
|
/**
|
|
753
|
* Very fast and dirty implementation to allow handling of transient objects as described in
|
|
754
|
* https://dev.e-taxonomy.eu/trac/ticket/3726
|
|
755
|
*
|
|
756
|
* Not yet complete.
|
|
757
|
*
|
|
758
|
* @param cdmBase
|
|
759
|
* @param state
|
|
760
|
*/
|
|
761
|
private void save(CdmBase cdmBase, Abcd206ImportState state) {
|
|
762
|
ICdmApplicationConfiguration cdmRepository = state.getConfig().getCdmAppController();
|
|
763
|
if (cdmRepository == null){
|
|
764
|
cdmRepository = this;
|
|
765
|
}
|
|
766
|
|
|
767
|
if (cdmBase.isInstanceOf(LanguageString.class)){
|
|
768
|
cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
|
|
769
|
}else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
|
|
770
|
cdmRepository.getOccurrenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class));
|
|
771
|
}else if (cdmBase.isInstanceOf(Reference.class)){
|
|
772
|
cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
|
|
773
|
}else if (cdmBase.isInstanceOf(Classification.class)){
|
|
774
|
cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
|
|
775
|
}else if (cdmBase.isInstanceOf(AgentBase.class)){
|
|
776
|
cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
|
|
777
|
}else if (cdmBase.isInstanceOf(Collection.class)){
|
|
778
|
cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
|
|
779
|
}else if (cdmBase.isInstanceOf(DescriptionBase.class)){
|
|
780
|
cdmRepository.getDescriptionService().saveOrUpdate(CdmBase.deproxy(cdmBase, DescriptionBase.class));
|
|
781
|
}else if (cdmBase.isInstanceOf(TaxonBase.class)){
|
|
782
|
cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
|
|
783
|
}else if (cdmBase.isInstanceOf(TaxonNameBase.class)){
|
|
784
|
cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNameBase.class));
|
|
785
|
}else{
|
|
786
|
throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
|
|
787
|
}
|
|
788
|
|
|
789
|
}
|
|
790
|
|
|
791
|
/**
|
|
792
|
* setCollectionData : store the collection object into the
|
|
793
|
* derivedUnitFacade
|
|
794
|
*
|
|
795
|
* @param state
|
|
796
|
*/
|
|
797
|
private void setCollectionData(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
|
|
798
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
799
|
AbcdImportUtility.setUnitID(derivedUnitFacade.innerDerivedUnit(), state.getDataHolder().unitID, config);
|
|
800
|
if(!config.isMapUnitIdToAccessionNumber()){
|
|
801
|
derivedUnitFacade.setAccessionNumber(NB(state.getDataHolder().accessionNumber));
|
|
802
|
}
|
|
803
|
// derivedUnitFacade.setCollectorsNumber(NB(state.getDataHolder().collectorsNumber));
|
|
804
|
|
|
805
|
/*
|
|
806
|
* INSTITUTION & COLLECTION
|
|
807
|
*/
|
|
808
|
// manage institution
|
|
809
|
Institution institution = this.getInstitution(NB(state.getDataHolder().institutionCode), state);
|
|
810
|
// manage collection
|
|
811
|
Collection collection = this.getCollection(institution, NB(state.getDataHolder().collectionCode), state);
|
|
812
|
// link specimen & collection
|
|
813
|
derivedUnitFacade.setCollection(collection);
|
|
814
|
}
|
|
815
|
|
|
816
|
/**
|
|
817
|
* getFacade : get the DerivedUnitFacade based on the recordBasis
|
|
818
|
* @param state
|
|
819
|
*
|
|
820
|
* @return DerivedUnitFacade
|
|
821
|
*/
|
|
822
|
private DerivedUnitFacade getFacade(Abcd206ImportState state) {
|
|
823
|
if(DEBUG) {
|
|
824
|
logger.info("getFacade()");
|
|
825
|
}
|
|
826
|
SpecimenOrObservationType type = null;
|
|
827
|
|
|
828
|
// create specimen
|
|
829
|
if (NB((state.getDataHolder().recordBasis)) != null) {
|
|
830
|
if (state.getDataHolder().recordBasis.toLowerCase().startsWith("s") || state.getDataHolder().recordBasis.toLowerCase().indexOf("specimen")>-1) {// specimen
|
|
831
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
832
|
}
|
|
833
|
if (state.getDataHolder().recordBasis.toLowerCase().startsWith("o") ||state.getDataHolder().recordBasis.toLowerCase().indexOf("observation")>-1 ) {
|
|
834
|
type = SpecimenOrObservationType.Observation;
|
|
835
|
}
|
|
836
|
if (state.getDataHolder().recordBasis.toLowerCase().indexOf("fossil")>-1){
|
|
837
|
type = SpecimenOrObservationType.Fossil;
|
|
838
|
}
|
|
839
|
if (state.getDataHolder().recordBasis.toLowerCase().indexOf("living")>-1) {
|
|
840
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
841
|
}
|
|
842
|
if (type == null) {
|
|
843
|
logger.info("The basis of record does not seem to be known: " + state.getDataHolder().recordBasis);
|
|
844
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
845
|
}
|
|
846
|
// TODO fossils?
|
|
847
|
} else {
|
|
848
|
logger.info("The basis of record is null");
|
|
849
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
850
|
}
|
|
851
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
852
|
return derivedUnitFacade;
|
|
853
|
}
|
|
854
|
|
|
855
|
private void getCollectorsFromXML(Element root, Abcd206XMLFieldGetter abcdFieldGetter, Abcd206ImportState state) {
|
|
856
|
NodeList group;
|
|
857
|
|
|
858
|
group = root.getChildNodes();
|
|
859
|
for (int i = 0; i < group.getLength(); i++) {
|
|
860
|
if (group.item(i).getNodeName().equals(state.getPrefix() + "Identifications")) {
|
|
861
|
group = group.item(i).getChildNodes();
|
|
862
|
break;
|
|
863
|
}
|
|
864
|
}
|
|
865
|
state.getDataHolder().gatheringAgentList = new ArrayList<String>();
|
|
866
|
state.getDataHolder().gatheringTeamList = new ArrayList<String>();
|
|
867
|
abcdFieldGetter.getType(root);
|
|
868
|
abcdFieldGetter.getGatheringPeople(root);
|
|
869
|
}
|
|
870
|
|
|
871
|
/**
|
|
872
|
* Store the unit's properties into variables Look which unit is the
|
|
873
|
* preferred one Look what kind of name it is supposed to be, for the
|
|
874
|
* parsing (Botanical, Zoological)
|
|
875
|
* @param state
|
|
876
|
*
|
|
877
|
* @param racine: the root node for a single unit
|
|
878
|
*/
|
|
879
|
private void setUnitPropertiesXML(Element root, Abcd206XMLFieldGetter abcdFieldGetter, Abcd206ImportState state) {
|
|
880
|
try {
|
|
881
|
NodeList group;
|
|
882
|
|
|
883
|
group = root.getChildNodes();
|
|
884
|
for (int i = 0; i < group.getLength(); i++) {
|
|
885
|
if (group.item(i).getNodeName().equals(state.getPrefix() + "Identifications")) {
|
|
886
|
group = group.item(i).getChildNodes();
|
|
887
|
break;
|
|
888
|
}
|
|
889
|
}
|
|
890
|
state.getDataHolder().identificationList = new ArrayList<Identification>();
|
|
891
|
state.getDataHolder().statusList = new ArrayList<SpecimenTypeDesignationStatus>();
|
|
892
|
state.getDataHolder().atomisedIdentificationList = new ArrayList<HashMap<String, String>>();
|
|
893
|
state.getDataHolder().referenceList = new ArrayList<String[]>();
|
|
894
|
state.getDataHolder().multimediaObjects = new ArrayList<String>();
|
|
895
|
|
|
896
|
abcdFieldGetter.getScientificNames(group);
|
|
897
|
abcdFieldGetter.getType(root);
|
|
898
|
|
|
899
|
if(DEBUG) {
|
|
900
|
logger.info("this.identificationList "+state.getDataHolder().identificationList.toString());
|
|
901
|
}
|
|
902
|
abcdFieldGetter.getIDs(root);
|
|
903
|
abcdFieldGetter.getRecordBasis(root);
|
|
904
|
abcdFieldGetter.getKindOfUnit(root);
|
|
905
|
abcdFieldGetter.getMultimedia(root);
|
|
906
|
abcdFieldGetter.getNumbers(root);
|
|
907
|
abcdFieldGetter.getGeolocation(root, state);
|
|
908
|
abcdFieldGetter.getGatheringPeople(root);
|
|
909
|
abcdFieldGetter.getGatheringDate(root);
|
|
910
|
abcdFieldGetter.getGatheringElevation(root);
|
|
911
|
abcdFieldGetter.getAssociatedUnitIds(root);
|
|
912
|
boolean referencefound = abcdFieldGetter.getReferences(root);
|
|
913
|
if (!referencefound) {
|
|
914
|
String[]a = {state.getRef().getTitleCache(),"",""};
|
|
915
|
state.getDataHolder().referenceList.add(a);
|
|
916
|
}
|
|
917
|
|
|
918
|
} catch (Exception e) {
|
|
919
|
logger.info("Error occured while parsing XML file" + e);
|
|
920
|
}
|
|
921
|
}
|
|
922
|
|
|
923
|
/**
|
|
924
|
* Look if the Institution does already exist
|
|
925
|
* @param institutionCode: a string with the institutioncode
|
|
926
|
* @param config : the configurator
|
|
927
|
* @return the Institution (existing or new)
|
|
928
|
*/
|
|
929
|
private Institution getInstitution(String institutionCode, Abcd206ImportState state) {
|
|
930
|
Institution institution=null;
|
|
931
|
List<Institution> institutions;
|
|
932
|
try {
|
|
933
|
institutions = getAgentService().list(Institution.class, null, null, null, null);
|
|
934
|
} catch (Exception e) {
|
|
935
|
institutions = new ArrayList<Institution>();
|
|
936
|
logger.warn(e);
|
|
937
|
}
|
|
938
|
if (institutions.size() > 0 && state.getConfig().isReUseExistingMetadata()) {
|
|
939
|
for (Institution institut:institutions){
|
|
940
|
try{
|
|
941
|
if (institut.getCode().equalsIgnoreCase(institutionCode)) {
|
|
942
|
institution=institut;
|
|
943
|
}
|
|
944
|
}catch(Exception e){logger.warn("no institution code in the db");}
|
|
945
|
}
|
|
946
|
}
|
|
947
|
if(DEBUG) {
|
|
948
|
if(institution !=null) {
|
|
949
|
logger.info("getinstitution " + institution.toString());
|
|
950
|
}
|
|
951
|
}
|
|
952
|
if (institution == null){
|
|
953
|
// create institution
|
|
954
|
institution = Institution.NewInstance();
|
|
955
|
institution.setCode(institutionCode);
|
|
956
|
institution.setTitleCache(institutionCode, true);
|
|
957
|
}
|
|
958
|
save(institution, state);
|
|
959
|
return institution;
|
|
960
|
}
|
|
961
|
|
|
962
|
/**
|
|
963
|
* Look if the Collection does already exist
|
|
964
|
* @param collectionCode
|
|
965
|
* @param collectionCode: a string
|
|
966
|
* @param config : the configurator
|
|
967
|
* @return the Collection (existing or new)
|
|
968
|
*/
|
|
969
|
private Collection getCollection(Institution institution, String collectionCode, Abcd206ImportState state) {
|
|
970
|
Collection collection = null;
|
|
971
|
List<Collection> collections;
|
|
972
|
try {
|
|
973
|
collections = getCollectionService().list(Collection.class, null, null, null, null);
|
|
974
|
} catch (Exception e) {
|
|
975
|
collections = new ArrayList<Collection>();
|
|
976
|
}
|
|
977
|
if (collections.size() > 0 && state.getConfig().isReUseExistingMetadata()) {
|
|
978
|
for (Collection coll:collections){
|
|
979
|
if (coll.getCode() != null && coll.getInstitute() != null
|
|
980
|
&& coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
|
|
981
|
collection = coll;
|
|
982
|
break;
|
|
983
|
}
|
|
984
|
}
|
|
985
|
}
|
|
986
|
|
|
987
|
if(collection == null){
|
|
988
|
collection =Collection.NewInstance();
|
|
989
|
collection.setCode(collectionCode);
|
|
990
|
collection.setInstitute(institution);
|
|
991
|
collection.setTitleCache(collectionCode);
|
|
992
|
}
|
|
993
|
save(collection, state);
|
|
994
|
return collection;
|
|
995
|
}
|
|
996
|
|
|
997
|
|
|
998
|
/**
|
|
999
|
* join DeterminationEvent to the Taxon Object
|
|
1000
|
* @param state : the ABCD import state
|
|
1001
|
* @param taxon: the current Taxon
|
|
1002
|
* @param preferredFlag :if the current name is preferred
|
|
1003
|
* @param derivedFacade : the derived Unit Facade
|
|
1004
|
*/
|
|
1005
|
@SuppressWarnings("rawtypes")
|
|
1006
|
private void linkDeterminationEvent(Abcd206ImportState state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade) {
|
|
1007
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
1008
|
if(DEBUG){
|
|
1009
|
logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
|
|
1010
|
}
|
|
1011
|
|
|
1012
|
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
|
|
1013
|
determinationEvent.setTaxonName(taxon.getName());
|
|
1014
|
determinationEvent.setPreferredFlag(preferredFlag);
|
|
1015
|
|
|
1016
|
determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
|
|
1017
|
state.getDerivedUnitBase().addDetermination(determinationEvent);
|
|
1018
|
|
|
1019
|
if(DEBUG){
|
|
1020
|
logger.info("NB TYPES INFO: "+ state.getDataHolder().statusList.size());
|
|
1021
|
}
|
|
1022
|
for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().statusList) {
|
|
1023
|
if (specimenTypeDesignationstatus != null) {
|
|
1024
|
if(DEBUG){
|
|
1025
|
logger.info("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
|
|
1026
|
}
|
|
1027
|
|
|
1028
|
ICdmApplicationConfiguration cdmAppController = config.getCdmAppController();
|
|
1029
|
if(cdmAppController == null){
|
|
1030
|
cdmAppController = this;
|
|
1031
|
}
|
|
1032
|
specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid());
|
|
1033
|
//Designation
|
|
1034
|
TaxonNameBase<?,?> name = taxon.getName();
|
|
1035
|
SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
|
|
1036
|
|
|
1037
|
designation.setTypeStatus(specimenTypeDesignationstatus);
|
|
1038
|
designation.setTypeSpecimen(state.getDerivedUnitBase());
|
|
1039
|
name.addTypeDesignation(designation, true);
|
|
1040
|
}
|
|
1041
|
}
|
|
1042
|
|
|
1043
|
for (String[] fullReference : state.getDataHolder().referenceList) {
|
|
1044
|
List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
|
|
1045
|
|
|
1046
|
String strReference=fullReference[0];
|
|
1047
|
String citationDetail = fullReference[1];
|
|
1048
|
String citationURL = fullReference[2];
|
|
1049
|
|
|
1050
|
if (isNotBlank(strReference)){
|
|
1051
|
Reference<?> reference = null;
|
|
1052
|
for (Reference<?> refe: references) {
|
|
1053
|
if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
|
|
1054
|
reference =refe;
|
|
1055
|
break;
|
|
1056
|
}
|
|
1057
|
}
|
|
1058
|
if (reference ==null){
|
|
1059
|
reference = ReferenceFactory.newGeneric();
|
|
1060
|
reference.setTitleCache(strReference, true);
|
|
1061
|
save(reference, state);
|
|
1062
|
}
|
|
1063
|
determinationEvent.addReference(reference);
|
|
1064
|
}
|
|
1065
|
}
|
|
1066
|
save(state.getDerivedUnitBase(), state);
|
|
1067
|
|
|
1068
|
if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
|
|
1069
|
//do not add IndividualsAssociation to non-preferred taxa
|
|
1070
|
if(DEBUG){
|
|
1071
|
logger.info("isDoCreateIndividualsAssociations");
|
|
1072
|
}
|
|
1073
|
|
|
1074
|
makeIndividualsAssociation(state, taxon, determinationEvent);
|
|
1075
|
|
|
1076
|
save(state.getDerivedUnitBase(), state);
|
|
1077
|
}
|
|
1078
|
}
|
|
1079
|
|
|
1080
|
/**
|
|
1081
|
* create and link each association (specimen, observation..) to the accepted taxon
|
|
1082
|
* @param state : the ABCD import state
|
|
1083
|
* @param taxon: the current Taxon
|
|
1084
|
* @param determinationEvent:the determinationevent
|
|
1085
|
*/
|
|
1086
|
private void makeIndividualsAssociation(Abcd206ImportState state, Taxon taxon, DeterminationEvent determinationEvent) {
|
|
1087
|
SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
|
|
1088
|
|
|
1089
|
if (DEBUG) {
|
|
1090
|
logger.info("MAKE INDIVIDUALS ASSOCIATION");
|
|
1091
|
}
|
|
1092
|
|
|
1093
|
TaxonDescription taxonDescription = null;
|
|
1094
|
Set<TaxonDescription> descriptions= taxon.getDescriptions();
|
|
1095
|
if (state.getConfig().isInteractWithUser()){
|
|
1096
|
if(!state.isDescriptionGroupSet()){
|
|
1097
|
taxonDescription = sui.askForDescriptionGroup(descriptions);
|
|
1098
|
state.setDescriptionGroup(taxonDescription);
|
|
1099
|
state.setDescriptionGroupSet(true);
|
|
1100
|
}else{
|
|
1101
|
taxonDescription=state.getDescriptionGroup();
|
|
1102
|
}
|
|
1103
|
} else {
|
|
1104
|
for (TaxonDescription description : descriptions){
|
|
1105
|
Set<IdentifiableSource> sources = description.getTaxon().getSources();
|
|
1106
|
sources.addAll(description.getSources());
|
|
1107
|
for (IdentifiableSource source:sources){
|
|
1108
|
if(state.getRef().equals(source.getCitation())) {
|
|
1109
|
taxonDescription = description;
|
|
1110
|
}
|
|
1111
|
}
|
|
1112
|
}
|
|
1113
|
}
|
|
1114
|
if (taxonDescription == null){
|
|
1115
|
taxonDescription = TaxonDescription.NewInstance(taxon, false);
|
|
1116
|
if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
|
|
1117
|
taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
|
|
1118
|
}
|
|
1119
|
state.setDescriptionGroup(taxonDescription);
|
|
1120
|
taxon.addDescription(taxonDescription);
|
|
1121
|
}
|
|
1122
|
|
|
1123
|
//PREPARE REFERENCE QUESTIONS
|
|
1124
|
|
|
1125
|
Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
|
|
1126
|
|
|
1127
|
List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
1128
|
List<DescriptionElementSource> issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
1129
|
|
|
1130
|
Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
|
|
1131
|
if(issTmp2!=null) {
|
|
1132
|
osbSet.addAll(issTmp2);
|
|
1133
|
}
|
|
1134
|
if(issTmp!=null) {
|
|
1135
|
osbSet.addAll(issTmp);
|
|
1136
|
}
|
|
1137
|
|
|
1138
|
|
|
1139
|
addToSourceMap(sourceMap, osbSet);
|
|
1140
|
|
|
1141
|
if (state.getConfig().isInteractWithUser()){
|
|
1142
|
List<OriginalSourceBase<?>> res = null;
|
|
1143
|
if(!state.isDescriptionSourcesSet()){
|
|
1144
|
res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
|
|
1145
|
"The current reference is "+state.getRef().getTitleCache(),getReferenceService(), state.getDataHolder().docSources);
|
|
1146
|
state.setDescriptionRefs(res);
|
|
1147
|
state.setDescriptionSourcesSet(true);
|
|
1148
|
}
|
|
1149
|
else{
|
|
1150
|
res=state.getDescriptionRefs();
|
|
1151
|
}
|
|
1152
|
if(res !=null) {
|
|
1153
|
for (OriginalSourceBase<?> sour:res){
|
|
1154
|
if(sour.isInstanceOf(IdentifiableSource.class)){
|
|
1155
|
try {
|
|
1156
|
if(sourceNotLinkedToElement(taxonDescription,sour)) {
|
|
1157
|
taxonDescription.addSource((IdentifiableSource)sour.clone());
|
|
1158
|
}
|
|
1159
|
} catch (CloneNotSupportedException e) {
|
|
1160
|
logger.warn("no cloning?");
|
|
1161
|
}
|
|
1162
|
}else{
|
|
1163
|
if(sourceNotLinkedToElement(taxonDescription,sour)) {
|
|
1164
|
taxonDescription.addSource(OriginalSourceType.Import,null, null, sour.getCitation(),sour.getCitationMicroReference());
|
|
1165
|
}
|
|
1166
|
}
|
|
1167
|
}
|
|
1168
|
}
|
|
1169
|
}
|
|
1170
|
else {
|
|
1171
|
if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
|
|
1172
|
taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1173
|
}
|
|
1174
|
}
|
|
1175
|
state.setDescriptionGroup(taxonDescription);
|
|
1176
|
|
|
1177
|
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
|
|
1178
|
Feature feature = makeFeature(state.getDerivedUnitBase());
|
|
1179
|
indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
|
|
1180
|
indAssociation.setFeature(feature);
|
|
1181
|
|
|
1182
|
if (state.getConfig().isInteractWithUser()){
|
|
1183
|
sourceMap = new HashMap<String, OriginalSourceBase<?>>();
|
|
1184
|
|
|
1185
|
issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
1186
|
issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
1187
|
|
|
1188
|
osbSet = new HashSet<OriginalSourceBase>();
|
|
1189
|
if(issTmp2!=null) {
|
|
1190
|
osbSet.addAll(issTmp2);
|
|
1191
|
}
|
|
1192
|
if(issTmp!=null) {
|
|
1193
|
osbSet.addAll(issTmp);
|
|
1194
|
}
|
|
1195
|
|
|
1196
|
|
|
1197
|
addToSourceMap(sourceMap, osbSet);
|
|
1198
|
|
|
1199
|
List<OriginalSourceBase<?>> sources =null;
|
|
1200
|
if(!state.isAssociationSourcesSet()) {
|
|
1201
|
sources = sui.askForSource(sourceMap, "descriptive element (association) ",taxon.toString(),
|
|
1202
|
getReferenceService(),state.getDataHolder().docSources);
|
|
1203
|
state.setAssociationRefs(sources);
|
|
1204
|
state.setAssociationSourcesSet(true);
|
|
1205
|
}
|
|
1206
|
else{
|
|
1207
|
sources=state.getAssociationRefs();
|
|
1208
|
}
|
|
1209
|
if(sources !=null) {
|
|
1210
|
for (OriginalSourceBase<?> source: sources) {
|
|
1211
|
if(source !=null) {
|
|
1212
|
if(source.isInstanceOf(DescriptionElementSource.class)){
|
|
1213
|
try {
|
|
1214
|
if(sourceNotLinkedToElement(indAssociation,source)) {
|
|
1215
|
indAssociation.addSource((DescriptionElementSource)source.clone());
|
|
1216
|
}
|
|
1217
|
} catch (CloneNotSupportedException e) {
|
|
1218
|
logger.warn("clone forbidden?");
|
|
1219
|
}
|
|
1220
|
}else{
|
|
1221
|
if(sourceNotLinkedToElement(indAssociation,source)) {
|
|
1222
|
indAssociation.addSource(OriginalSourceType.Import,null, null, source.getCitation(),source.getCitationMicroReference());
|
|
1223
|
}
|
|
1224
|
try {
|
|
1225
|
if(sourceNotLinkedToElement(state.getDerivedUnitBase(), source)) {
|
|
1226
|
state.getDerivedUnitBase().addSource((IdentifiableSource) source.clone());
|
|
1227
|
}
|
|
1228
|
} catch (CloneNotSupportedException e) {
|
|
1229
|
// TODO Auto-generated catch block
|
|
1230
|
e.printStackTrace();
|
|
1231
|
}
|
|
1232
|
}
|
|
1233
|
|
|
1234
|
}
|
|
1235
|
}
|
|
1236
|
}
|
|
1237
|
}else {
|
|
1238
|
if(sourceNotLinkedToElement(indAssociation,state.getRef(),null)) {
|
|
1239
|
indAssociation.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1240
|
}
|
|
1241
|
if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
|
|
1242
|
state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1243
|
}
|
|
1244
|
for (Reference<?> citation : determinationEvent.getReferences()) {
|
|
1245
|
if(sourceNotLinkedToElement(indAssociation,citation,null))
|
|
1246
|
{
|
|
1247
|
indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
|
|
1248
|
}
|
|
1249
|
if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
|
|
1250
|
state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
|
|
1251
|
}
|
|
1252
|
}
|
|
1253
|
}
|
|
1254
|
|
|
1255
|
taxonDescription.addElement(indAssociation);
|
|
1256
|
|
|
1257
|
save(taxonDescription, state);
|
|
1258
|
save(taxon, state);
|
|
1259
|
report.addDerivate(state.getDerivedUnitBase(), state.getConfig());
|
|
1260
|
report.addIndividualAssociation(taxon, state.getDataHolder().unitID, state.getDerivedUnitBase());
|
|
1261
|
}
|
|
1262
|
|
|
1263
|
/**
|
|
1264
|
* @param derivedUnitBase2
|
|
1265
|
* @param ref2
|
|
1266
|
* @param object
|
|
1267
|
* @return
|
|
1268
|
*/
|
|
1269
|
private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference<?> b, String d) {
|
|
1270
|
Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
|
|
1271
|
for (IdentifiableSource is:linkedSources){
|
|
1272
|
Reference<?> a = is.getCitation();
|
|
1273
|
String c = is.getCitationMicroReference();
|
|
1274
|
|
|
1275
|
boolean refMatch=false;
|
|
1276
|
boolean microMatch=false;
|
|
1277
|
|
|
1278
|
try{
|
|
1279
|
if (a==null && b==null) {
|
|
1280
|
refMatch=true;
|
|
1281
|
}
|
|
1282
|
if (a!=null && b!=null) {
|
|
1283
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1284
|
refMatch=true;
|
|
1285
|
}
|
|
1286
|
}
|
|
1287
|
}catch(Exception e){}
|
|
1288
|
|
|
1289
|
|
|
1290
|
try{
|
|
1291
|
if (c==null && d==null) {
|
|
1292
|
microMatch=true;
|
|
1293
|
}
|
|
1294
|
if(c!=null && d!=null) {
|
|
1295
|
if(c.equalsIgnoreCase(d)) {
|
|
1296
|
microMatch=true;
|
|
1297
|
}
|
|
1298
|
}
|
|
1299
|
}
|
|
1300
|
catch(Exception e){}
|
|
1301
|
|
|
1302
|
if (microMatch && refMatch) {
|
|
1303
|
return false;
|
|
1304
|
}
|
|
1305
|
|
|
1306
|
|
|
1307
|
}
|
|
1308
|
return true;
|
|
1309
|
}
|
|
1310
|
|
|
1311
|
/**
|
|
1312
|
* @param specimen
|
|
1313
|
* @param source
|
|
1314
|
* @return
|
|
1315
|
*/
|
|
1316
|
private boolean sourceNotLinkedToElement(SpecimenOrObservationBase<?> specimen, OriginalSourceBase<?> source) {
|
|
1317
|
Set<IdentifiableSource> linkedSources = specimen.getSources();
|
|
1318
|
for (IdentifiableSource is:linkedSources){
|
|
1319
|
Reference<?> a = is.getCitation();
|
|
1320
|
Reference<?> b = source.getCitation();
|
|
1321
|
String c = is.getCitationMicroReference();
|
|
1322
|
String d = source.getCitationMicroReference();
|
|
1323
|
|
|
1324
|
boolean refMatch=false;
|
|
1325
|
boolean microMatch=false;
|
|
1326
|
|
|
1327
|
try{
|
|
1328
|
if (a==null && b==null) {
|
|
1329
|
refMatch=true;
|
|
1330
|
}
|
|
1331
|
if (a!=null && b!=null) {
|
|
1332
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1333
|
refMatch=true;
|
|
1334
|
}
|
|
1335
|
}
|
|
1336
|
}catch(Exception e){}
|
|
1337
|
|
|
1338
|
|
|
1339
|
try{
|
|
1340
|
if (c==null && d==null) {
|
|
1341
|
microMatch=true;
|
|
1342
|
}
|
|
1343
|
if(c!=null && d!=null) {
|
|
1344
|
if(c.equalsIgnoreCase(d)) {
|
|
1345
|
microMatch=true;
|
|
1346
|
}
|
|
1347
|
}
|
|
1348
|
}
|
|
1349
|
catch(Exception e){}
|
|
1350
|
|
|
1351
|
if (microMatch && refMatch) {
|
|
1352
|
return false;
|
|
1353
|
}
|
|
1354
|
|
|
1355
|
|
|
1356
|
}
|
|
1357
|
return true;
|
|
1358
|
}
|
|
1359
|
|
|
1360
|
/**
|
|
1361
|
* @param indAssociation
|
|
1362
|
* @param ref2
|
|
1363
|
* @param object
|
|
1364
|
* @return
|
|
1365
|
*/
|
|
1366
|
private boolean sourceNotLinkedToElement(IndividualsAssociation indAssociation, Reference<?> a, String d) {
|
|
1367
|
Set<DescriptionElementSource> linkedSources = indAssociation.getSources();
|
|
1368
|
for (DescriptionElementSource is:linkedSources){
|
|
1369
|
Reference<?> b = is.getCitation();
|
|
1370
|
String c = is.getCitationMicroReference();
|
|
1371
|
|
|
1372
|
boolean refMatch=false;
|
|
1373
|
boolean microMatch=false;
|
|
1374
|
|
|
1375
|
try{
|
|
1376
|
if (a==null && b==null) {
|
|
1377
|
refMatch=true;
|
|
1378
|
}
|
|
1379
|
if (a!=null && b!=null) {
|
|
1380
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1381
|
refMatch=true;
|
|
1382
|
}
|
|
1383
|
}
|
|
1384
|
}catch(Exception e){}
|
|
1385
|
|
|
1386
|
|
|
1387
|
try{
|
|
1388
|
if (c==null && d==null) {
|
|
1389
|
microMatch=true;
|
|
1390
|
}
|
|
1391
|
if(c!=null && d!=null) {
|
|
1392
|
if(c.equalsIgnoreCase(d)) {
|
|
1393
|
microMatch=true;
|
|
1394
|
}
|
|
1395
|
}
|
|
1396
|
}
|
|
1397
|
catch(Exception e){}
|
|
1398
|
|
|
1399
|
if (microMatch && refMatch) {
|
|
1400
|
return false;
|
|
1401
|
}
|
|
1402
|
}
|
|
1403
|
return true;
|
|
1404
|
}
|
|
1405
|
|
|
1406
|
/**
|
|
1407
|
* @param taxonDescription
|
|
1408
|
* @param ref2
|
|
1409
|
* @param object
|
|
1410
|
* @return
|
|
1411
|
*/
|
|
1412
|
private boolean sourceNotLinkedToElement(TaxonDescription taxonDescription, Reference<?> a, String d) {
|
|
1413
|
Set<IdentifiableSource> linkedSources = taxonDescription.getSources();
|
|
1414
|
for (IdentifiableSource is:linkedSources){
|
|
1415
|
Reference<?> b = is.getCitation();
|
|
1416
|
String c = is.getCitationMicroReference();
|
|
1417
|
|
|
1418
|
boolean refMatch=false;
|
|
1419
|
boolean microMatch=false;
|
|
1420
|
|
|
1421
|
try{
|
|
1422
|
if (a==null && b==null) {
|
|
1423
|
refMatch=true;
|
|
1424
|
}
|
|
1425
|
if (a!=null && b!=null) {
|
|
1426
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1427
|
refMatch=true;
|
|
1428
|
}
|
|
1429
|
}
|
|
1430
|
}catch(Exception e){}
|
|
1431
|
|
|
1432
|
|
|
1433
|
try{
|
|
1434
|
if (c==null && d==null) {
|
|
1435
|
microMatch=true;
|
|
1436
|
}
|
|
1437
|
if(c!=null && d!=null) {
|
|
1438
|
if(c.equalsIgnoreCase(d)) {
|
|
1439
|
microMatch=true;
|
|
1440
|
}
|
|
1441
|
}
|
|
1442
|
}
|
|
1443
|
catch(Exception e){}
|
|
1444
|
|
|
1445
|
if (microMatch && refMatch) {
|
|
1446
|
return false;
|
|
1447
|
}
|
|
1448
|
}
|
|
1449
|
return true;
|
|
1450
|
}
|
|
1451
|
|
|
1452
|
/**
|
|
1453
|
* @param indAssociation
|
|
1454
|
* @param source
|
|
1455
|
* @return
|
|
1456
|
*/
|
|
1457
|
private boolean sourceNotLinkedToElement(IndividualsAssociation indAssociation, OriginalSourceBase<?> source) {
|
|
1458
|
Set<DescriptionElementSource> linkedSources = indAssociation.getSources();
|
|
1459
|
for (DescriptionElementSource is:linkedSources){
|
|
1460
|
Reference<?> a = is.getCitation();
|
|
1461
|
Reference<?> b = source.getCitation();
|
|
1462
|
String c = is.getCitationMicroReference();
|
|
1463
|
String d = source.getCitationMicroReference();
|
|
1464
|
|
|
1465
|
boolean refMatch=false;
|
|
1466
|
boolean microMatch=false;
|
|
1467
|
|
|
1468
|
try{
|
|
1469
|
if (a==null && b==null) {
|
|
1470
|
refMatch=true;
|
|
1471
|
}
|
|
1472
|
if (a!=null && b!=null) {
|
|
1473
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1474
|
refMatch=true;
|
|
1475
|
}
|
|
1476
|
}
|
|
1477
|
}catch(Exception e){}
|
|
1478
|
|
|
1479
|
|
|
1480
|
try{
|
|
1481
|
if (c==null && d==null) {
|
|
1482
|
microMatch=true;
|
|
1483
|
}
|
|
1484
|
if(c!=null && d!=null) {
|
|
1485
|
if(c.equalsIgnoreCase(d)) {
|
|
1486
|
microMatch=true;
|
|
1487
|
}
|
|
1488
|
}
|
|
1489
|
}
|
|
1490
|
catch(Exception e){}
|
|
1491
|
|
|
1492
|
if (microMatch && refMatch) {
|
|
1493
|
return false;
|
|
1494
|
}
|
|
1495
|
}
|
|
1496
|
return true;
|
|
1497
|
}
|
|
1498
|
|
|
1499
|
/**
|
|
1500
|
* @param taxonDescription
|
|
1501
|
* @param sour
|
|
1502
|
* @return
|
|
1503
|
*/
|
|
1504
|
private boolean sourceNotLinkedToElement(TaxonDescription taxonDescription, OriginalSourceBase<?> sour) {
|
|
1505
|
Set<IdentifiableSource> linkedSources = taxonDescription.getSources();
|
|
1506
|
for (IdentifiableSource is:linkedSources){
|
|
1507
|
Reference<?> a = is.getCitation();
|
|
1508
|
Reference<?> b = sour.getCitation();
|
|
1509
|
String c = is.getCitationMicroReference();
|
|
1510
|
String d = sour.getCitationMicroReference();
|
|
1511
|
|
|
1512
|
boolean refMatch=false;
|
|
1513
|
boolean microMatch=false;
|
|
1514
|
|
|
1515
|
try{
|
|
1516
|
if (a==null && b==null) {
|
|
1517
|
refMatch=true;
|
|
1518
|
}
|
|
1519
|
if (a!=null && b!=null) {
|
|
1520
|
if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
|
|
1521
|
refMatch=true;
|
|
1522
|
}
|
|
1523
|
}
|
|
1524
|
}catch(Exception e){}
|
|
1525
|
|
|
1526
|
|
|
1527
|
try{
|
|
1528
|
if (c==null && d==null) {
|
|
1529
|
microMatch=true;
|
|
1530
|
}
|
|
1531
|
if(c!=null && d!=null) {
|
|
1532
|
if(c.equalsIgnoreCase(d)) {
|
|
1533
|
microMatch=true;
|
|
1534
|
}
|
|
1535
|
}
|
|
1536
|
}
|
|
1537
|
catch(Exception e){}
|
|
1538
|
|
|
1539
|
if (microMatch && refMatch) {
|
|
1540
|
return false;
|
|
1541
|
}
|
|
1542
|
|
|
1543
|
|
|
1544
|
}
|
|
1545
|
return true;
|
|
1546
|
}
|
|
1547
|
|
|
1548
|
/**
|
|
1549
|
* look for the Feature object (FieldObs, Specimen,...)
|
|
1550
|
* @param unit : a specimen or obersvation base
|
|
1551
|
* @return the corresponding Feature
|
|
1552
|
*/
|
|
1553
|
private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
|
|
1554
|
SpecimenOrObservationType type = unit.getRecordBasis();
|
|
1555
|
|
|
1556
|
|
|
1557
|
|
|
1558
|
if (type.isFeatureObservation()){
|
|
1559
|
return Feature.OBSERVATION();
|
|
1560
|
}else if (type.isFeatureSpecimen()){
|
|
1561
|
return Feature.SPECIMEN();
|
|
1562
|
}else if (type == SpecimenOrObservationType.DerivedUnit){
|
|
1563
|
return Feature.OBSERVATION();
|
|
1564
|
// return getFeature("Specimen or observation");
|
|
1565
|
}else{
|
|
1566
|
String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
|
|
1567
|
logger.warn(String.format(message, type.getMessage()));
|
|
1568
|
return Feature.OBSERVATION();
|
|
1569
|
// return getFeature("Specimen or observation");
|
|
1570
|
|
|
1571
|
}
|
|
1572
|
}
|
|
1573
|
|
|
1574
|
/**
|
|
1575
|
* HandleIdentifications : get the scientific names present in the ABCD
|
|
1576
|
* document and store link them with the observation/specimen data
|
|
1577
|
* @param state: the current ABCD import state
|
|
1578
|
* @param derivedUnitFacade : the current derivedunitfacade
|
|
1579
|
*/
|
|
1580
|
private void handleIdentifications(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
|
|
1581
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
1582
|
|
|
1583
|
|
|
1584
|
String scientificName = "";
|
|
1585
|
boolean preferredFlag = false;
|
|
1586
|
|
|
1587
|
if (state.getDataHolder().nomenclatureCode == ""){
|
|
1588
|
state.getDataHolder().nomenclatureCode = config.getNomenclaturalCode().toString();
|
|
1589
|
}
|
|
1590
|
|
|
1591
|
for (int i = 0; i < state.getDataHolder().identificationList.size(); i++) {
|
|
1592
|
Identification identification = state.getDataHolder().identificationList.get(i);
|
|
1593
|
scientificName = identification.getScientificName().replaceAll(" et ", " & ");
|
|
1594
|
|
|
1595
|
String preferred = identification.getPreferred();
|
|
1596
|
if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || state.getDataHolder().identificationList.size()==1) {
|
|
1597
|
preferredFlag = true;
|
|
1598
|
}
|
|
1599
|
else {
|
|
1600
|
preferredFlag = false;
|
|
1601
|
}
|
|
1602
|
|
|
1603
|
if (identification.getCode().indexOf(':') != -1) {
|
|
1604
|
state.getDataHolder().nomenclatureCode = identification.getCode().split(COLON)[1];
|
|
1605
|
}
|
|
1606
|
else{
|
|
1607
|
state.getDataHolder().nomenclatureCode = identification.getCode();
|
|
1608
|
}
|
|
1609
|
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
|
|
1610
|
Taxon taxon = getOrCreateTaxonForName(taxonName, state);
|
|
1611
|
addTaxonNode(taxon, state,preferredFlag);
|
|
1612
|
linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade);
|
|
1613
|
}
|
|
1614
|
}
|
|
1615
|
|
|
1616
|
|
|
1617
|
private TaxonNameBase<?, ?> getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, Abcd206ImportState state, int unitIndexInAbcdFile){
|
|
1618
|
TaxonNameBase<?, ?> taxonName = null;
|
|
1619
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
1620
|
|
|
1621
|
//check atomised name data for rank
|
|
1622
|
//new name will be created
|
|
1623
|
NonViralName<?> atomisedTaxonName = null;
|
|
1624
|
if (rank==null && unitIndexInAbcdFile>=0 && (state.getDataHolder().atomisedIdentificationList != null || state.getDataHolder().atomisedIdentificationList.size() > 0)) {
|
|
1625
|
atomisedTaxonName = setTaxonNameByType(state.getDataHolder().atomisedIdentificationList.get(unitIndexInAbcdFile), scientificName, state);
|
|
1626
|
if(atomisedTaxonName!=null){
|
|
1627
|
rank = atomisedTaxonName.getRank();
|
|
1628
|
}
|
|
1629
|
}
|
|
1630
|
if(config.isReuseExistingTaxaWhenPossible()){
|
|
1631
|
NonViralName<?> parsedName = atomisedTaxonName;
|
|
1632
|
if(parsedName==null){
|
|
1633
|
parsedName = parseScientificName(scientificName, state, report);
|
|
1634
|
}
|
|
1635
|
if(config.isIgnoreAuthorship() && parsedName!=null && preferredFlag){
|
|
1636
|
// do not ignore authorship for non-preferred names because they need
|
|
1637
|
// to be created for the determination history
|
|
1638
|
String nameCache = parsedName.getNameCache();
|
|
1639
|
List<NonViralName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
|
|
1640
|
taxonName = getBestMatchingName(scientificName, new ArrayList<TaxonNameBase>(names));
|
|
1641
|
}
|
|
1642
|
else {
|
|
1643
|
//search for existing names
|
|
1644
|
List<TaxonNameBase> names = getNameService().listByTitle(TaxonNameBase.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
|
|
1645
|
taxonName = getBestMatchingName(scientificName, names);
|
|
1646
|
//still nothing found -> try with the atomised name full title cache
|
|
1647
|
if(taxonName==null && atomisedTaxonName!=null){
|
|
1648
|
names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
|
|
1649
|
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names);
|
|
1650
|
//still nothing found -> try with the atomised name title cache
|
|
1651
|
if(taxonName==null){
|
|
1652
|
names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
|
|
1653
|
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names);
|
|
1654
|
}
|
|
1655
|
}
|
|
1656
|
}
|
|
1657
|
}
|
|
1658
|
|
|
1659
|
if(taxonName==null && atomisedTaxonName!=null){
|
|
1660
|
taxonName = atomisedTaxonName;
|
|
1661
|
report.addName(taxonName);
|
|
1662
|
logger.info("Created new taxon name "+taxonName);
|
|
1663
|
if(taxonName.hasProblem()){
|
|
1664
|
report.addInfoMessage(String.format("Created %s with parsing problems", taxonName));
|
|
1665
|
}
|
|
1666
|
if(!atomisedTaxonName.getTitleCache().equals(scientificName)){
|
|
1667
|
report.addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
|
|
1668
|
}
|
|
1669
|
}
|
|
1670
|
else if(taxonName==null){
|
|
1671
|
//create new taxon name
|
|
1672
|
taxonName = NonViralName.NewInstance(rank);
|
|
1673
|
taxonName.setFullTitleCache(scientificName,true);
|
|
1674
|
taxonName.setTitleCache(scientificName, true);
|
|
1675
|
report.addName(taxonName);
|
|
1676
|
logger.info("Created new taxon name "+taxonName);
|
|
1677
|
}
|
|
1678
|
save(taxonName, state);
|
|
1679
|
return taxonName;
|
|
1680
|
}
|
|
1681
|
|
|
1682
|
private TaxonNameBase<?, ?> getBestMatchingName(String scientificName, java.util.Collection<TaxonNameBase> names){
|
|
1683
|
List<TaxonNameBase> namesWithAcceptedTaxa = new ArrayList<TaxonNameBase>();
|
|
1684
|
for (TaxonNameBase name : names) {
|
|
1685
|
if(!name.getTaxa().isEmpty()){
|
|
1686
|
namesWithAcceptedTaxa.add(name);
|
|
1687
|
}
|
|
1688
|
}
|
|
1689
|
String message = "More than one taxon name was found for "+scientificName+"!";
|
|
1690
|
//check for names with accepted taxa
|
|
1691
|
if(namesWithAcceptedTaxa.size()>0){
|
|
1692
|
if(namesWithAcceptedTaxa.size()>1){
|
|
1693
|
report.addInfoMessage(message);
|
|
1694
|
logger.warn(message);
|
|
1695
|
return null;
|
|
1696
|
}
|
|
1697
|
return namesWithAcceptedTaxa.iterator().next();
|
|
1698
|
}
|
|
1699
|
//no names with accepted taxa found -> check accepted taxa of synonyms
|
|
1700
|
List<Taxon> taxaFromSynonyms = new ArrayList<Taxon>();
|
|
1701
|
for (TaxonNameBase name : names) {
|
|
1702
|
Set<TaxonBase> taxonBases = name.getTaxonBases();
|
|
1703
|
for (TaxonBase taxonBase : taxonBases) {
|
|
1704
|
if(taxonBase.isInstanceOf(Synonym.class)){
|
|
1705
|
Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
|
|
1706
|
taxaFromSynonyms.addAll(synonym.getAcceptedTaxa());
|
|
1707
|
}
|
|
1708
|
}
|
|
1709
|
}
|
|
1710
|
if(taxaFromSynonyms.size()>0){
|
|
1711
|
if(taxaFromSynonyms.size()>1){
|
|
1712
|
report.addInfoMessage(message);
|
|
1713
|
logger.warn(message);
|
|
1714
|
return null;
|
|
1715
|
}
|
|
1716
|
return taxaFromSynonyms.iterator().next().getName();
|
|
1717
|
}
|
|
1718
|
return null;
|
|
1719
|
}
|
|
1720
|
|
|
1721
|
private Taxon getOrCreateTaxonForName(TaxonNameBase<?, ?> taxonNameBase, Abcd206ImportState state){
|
|
1722
|
Set<Taxon> acceptedTaxa = taxonNameBase.getTaxa();
|
|
1723
|
if(acceptedTaxa.size()>0){
|
|
1724
|
Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
|
|
1725
|
if(acceptedTaxa.size()>1){
|
|
1726
|
String message = "More than one accepted taxon was found for taxon name: "
|
|
1727
|
+ taxonNameBase.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
|
|
1728
|
report.addInfoMessage(message);
|
|
1729
|
logger.warn(message);
|
|
1730
|
}
|
|
1731
|
else{
|
|
1732
|
return firstAcceptedTaxon;
|
|
1733
|
}
|
|
1734
|
}
|
|
1735
|
else{
|
|
1736
|
Set<TaxonBase> taxonAndSynonyms = taxonNameBase.getTaxonBases();
|
|
1737
|
for (TaxonBase taxonBase : taxonAndSynonyms) {
|
|
1738
|
if(taxonBase.isInstanceOf(Synonym.class)){
|
|
1739
|
Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
|
|
1740
|
Set<Taxon> acceptedTaxaOfSynonym = synonym.getAcceptedTaxa();
|
|
1741
|
if(acceptedTaxaOfSynonym.size()!=1){
|
|
1742
|
String message = "No accepted taxa could be found for taxon name: "
|
|
1743
|
+ taxonNameBase.getTitleCache()
|
|
1744
|
+ "!\nEither it is a pro parte synonym or has no accepted taxa";
|
|
1745
|
report.addInfoMessage(message);
|
|
1746
|
logger.warn(message);
|
|
1747
|
}
|
|
1748
|
else{
|
|
1749
|
return acceptedTaxaOfSynonym.iterator().next();
|
|
1750
|
}
|
|
1751
|
}
|
|
1752
|
}
|
|
1753
|
}
|
|
1754
|
Taxon taxon = Taxon.NewInstance(taxonNameBase, state.getRef());
|
|
1755
|
save(taxon, state);
|
|
1756
|
report.addTaxon(taxon);
|
|
1757
|
logger.info("Created new taxon "+ taxon);
|
|
1758
|
return taxon;
|
|
1759
|
}
|
|
1760
|
|
|
1761
|
/**
|
|
1762
|
* @param taxon : a taxon to add as a node
|
|
1763
|
* @param state : the ABCD import state
|
|
1764
|
*/
|
|
1765
|
private void addTaxonNode(Taxon taxon, Abcd206ImportState state, boolean preferredFlag) {
|
|
1766
|
logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
|
|
1767
|
//only add nodes if not already existing in current classification or default classification
|
|
1768
|
|
|
1769
|
//check if node exists in current classification
|
|
1770
|
//NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
|
|
1771
|
if (!existsInClassification(taxon, state.getClassification())){
|
|
1772
|
if(state.getConfig().isMoveNewTaxaToDefaultClassification()){
|
|
1773
|
//check if node exists in default classification
|
|
1774
|
if(!existsInClassification(taxon, state.getDefaultClassification())){
|
|
1775
|
addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification());
|
|
1776
|
}
|
|
1777
|
}
|
|
1778
|
else {
|
|
1779
|
//add non-existing taxon to current classification
|
|
1780
|
addParentTaxon(taxon, state, preferredFlag, state.getClassification());
|
|
1781
|
}
|
|
1782
|
}
|
|
1783
|
}
|
|
1784
|
|
|
1785
|
private boolean existsInClassification(Taxon taxon, Classification classification){
|
|
1786
|
boolean exist = false;
|
|
1787
|
Set<TaxonNode> allNodes = classification.getAllNodes();
|
|
1788
|
for (TaxonNode p : allNodes){
|
|
1789
|
try{
|
|
1790
|
if(p.getTaxon().equals(taxon)) {
|
|
1791
|
exist = true;
|
|
1792
|
}
|
|
1793
|
}
|
|
1794
|
catch(Exception e){
|
|
1795
|
logger.warn("TaxonNode doesn't seem to have a taxon");
|
|
1796
|
}
|
|
1797
|
}
|
|
1798
|
return exist;
|
|
1799
|
}
|
|
1800
|
|
|
1801
|
private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
|
|
1802
|
if(taxon.getTaxonNodes()!=null){
|
|
1803
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
1804
|
if(node.getClassification().equals(classification)){
|
|
1805
|
return true;
|
|
1806
|
}
|
|
1807
|
}
|
|
1808
|
}
|
|
1809
|
return false;
|
|
1810
|
}
|
|
1811
|
|
|
1812
|
/**
|
|
1813
|
* Add the hierarchy for a Taxon(add higher taxa)
|
|
1814
|
* @param classification
|
|
1815
|
* @param taxon: a taxon to add as a node
|
|
1816
|
* @param state: the ABCD import state
|
|
1817
|
*/
|
|
1818
|
private void addParentTaxon(Taxon taxon, Abcd206ImportState state, boolean preferredFlag, Classification classification){
|
|
1819
|
NonViralName<?> nvname = CdmBase.deproxy(taxon.getName(), NonViralName.class);
|
|
1820
|
Rank rank = nvname.getRank();
|
|
1821
|
Taxon genus =null;
|
|
1822
|
Taxon subgenus =null;
|
|
1823
|
Taxon species = null;
|
|
1824
|
Taxon subspecies = null;
|
|
1825
|
Taxon parent = null;
|
|
1826
|
if(rank!=null){
|
|
1827
|
if (rank.isLower(Rank.GENUS() )){
|
|
1828
|
String genusOrUninomial = nvname.getGenusOrUninomial();
|
|
1829
|
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
|
|
1830
|
genus = getOrCreateTaxonForName(taxonName, state);
|
|
1831
|
if (preferredFlag) {
|
|
1832
|
parent = linkParentChildNode(null, genus, classification, state);
|
|
1833
|
}
|
|
1834
|
|
|
1835
|
}
|
|
1836
|
if (rank.isLower(Rank.SUBGENUS())){
|
|
1837
|
String prefix = nvname.getGenusOrUninomial();
|
|
1838
|
String name = nvname.getInfraGenericEpithet();
|
|
1839
|
if (name != null){
|
|
1840
|
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
|
|
1841
|
subgenus = getOrCreateTaxonForName(taxonName, state);
|
|
1842
|
if (preferredFlag) {
|
|
1843
|
parent = linkParentChildNode(genus, subgenus, classification, state);
|
|
1844
|
} }
|
|
1845
|
}
|
|
1846
|
if (rank.isLower(Rank.SPECIES())){
|
|
1847
|
if (subgenus!=null){
|
|
1848
|
String prefix = nvname.getGenusOrUninomial();
|
|
1849
|
String name = nvname.getInfraGenericEpithet();
|
|
1850
|
String spe = nvname.getSpecificEpithet();
|
|
1851
|
if (spe != null){
|
|
1852
|
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
|
|
1853
|
species = getOrCreateTaxonForName(taxonName, state);
|
|
1854
|
if (preferredFlag) {
|
|
1855
|
parent = linkParentChildNode(subgenus, species, classification, state);
|
|
1856
|
}
|
|
1857
|
}
|
|
1858
|
}
|
|
1859
|
else{
|
|
1860
|
String prefix = nvname.getGenusOrUninomial();
|
|
1861
|
String name = nvname.getSpecificEpithet();
|
|
1862
|
if (name != null){
|
|
1863
|
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
|
|
1864
|
species = getOrCreateTaxonForName(taxonName, state);
|
|
1865
|
if (preferredFlag) {
|
|
1866
|
parent = linkParentChildNode(genus, species, classification, state);
|
|
1867
|
}
|
|
1868
|
}
|
|
1869
|
}
|
|
1870
|
}
|
|
1871
|
if (rank.isLower(Rank.INFRASPECIES())){
|
|
1872
|
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
|
|
1873
|
subspecies = getOrCreateTaxonForName(taxonName, state);
|
|
1874
|
if (preferredFlag) {
|
|
1875
|
parent = linkParentChildNode(species, subspecies, classification, state);
|
|
1876
|
}
|
|
1877
|
}
|
|
1878
|
}
|
|
1879
|
if (preferredFlag && parent!=taxon) {
|
|
1880
|
linkParentChildNode(parent, taxon, classification, state);
|
|
1881
|
}
|
|
1882
|
}
|
|
1883
|
|
|
1884
|
/**
|
|
1885
|
* Link a parent to a child and save it in the current classification
|
|
1886
|
* @param parent: the higher Taxon
|
|
1887
|
* @param child : the lower (or current) Taxon
|
|
1888
|
* return the Taxon from the new created Node
|
|
1889
|
* @param classification
|
|
1890
|
* @param state
|
|
1891
|
*/
|
|
1892
|
private Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, Abcd206ImportState state) {
|
|
1893
|
TaxonNode node =null;
|
|
1894
|
if (parent != null) {
|
|
1895
|
parent = (Taxon) getTaxonService().find(parent.getUuid());
|
|
1896
|
child = (Taxon) getTaxonService().find(child.getUuid());
|
|
1897
|
//here we do not have to check if the taxon nodes already exists
|
|
1898
|
//this is done by classification.addParentChild()
|
|
1899
|
//do not add child node if it already exists
|
|
1900
|
if(hasTaxonNodeInClassification(child, classification)){
|
|
1901
|
return child;
|
|
1902
|
}
|
|
1903
|
else{
|
|
1904
|
node = classification.addParentChild(parent, child, state.getRef(), "");
|
|
1905
|
save(classification, state);
|
|
1906
|
}
|
|
1907
|
}
|
|
1908
|
else {
|
|
1909
|
child = (Taxon) getTaxonService().find(child.getUuid());
|
|
1910
|
//do not add child node if it already exists
|
|
1911
|
if(hasTaxonNodeInClassification(child, classification)){
|
|
1912
|
return child;
|
|
1913
|
}
|
|
1914
|
else{
|
|
1915
|
node = classification.addChildTaxon(child, state.getRef(), null);
|
|
1916
|
save(classification, state);
|
|
1917
|
}
|
|
1918
|
}
|
|
1919
|
if(node!=null){
|
|
1920
|
report.addTaxonNode(node);
|
|
1921
|
return node.getTaxon();
|
|
1922
|
}
|
|
1923
|
String message = "Could not create taxon node for " +child;
|
|
1924
|
report.addInfoMessage(message);
|
|
1925
|
logger.warn(message);
|
|
1926
|
return null;
|
|
1927
|
}
|
|
1928
|
|
|
1929
|
/**
|
|
1930
|
* Parse automatically the scientific name
|
|
1931
|
* @param scientificName the scientific name to parse
|
|
1932
|
* @param state the current import state
|
|
1933
|
* @param report the import report
|
|
1934
|
* @return a parsed name
|
|
1935
|
*/
|
|
1936
|
private NonViralName<?> parseScientificName(String scientificName, Abcd206ImportState state, Abcd206ImportReport report) {
|
|
1937
|
NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
|
|
1938
|
NonViralName<?> taxonName = null;
|
|
1939
|
boolean problem = false;
|
|
1940
|
|
|
1941
|
if(DEBUG){
|
|
1942
|
logger.info("parseScientificName " + state.getDataHolder().nomenclatureCode.toString());
|
|
1943
|
}
|
|
1944
|
|
|
1945
|
if (state.getDataHolder().nomenclatureCode.toString().equals("Zoological") || state.getDataHolder().nomenclatureCode.toString().contains("ICZN")) {
|
|
1946
|
taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, null);
|
|
1947
|
if (taxonName.hasProblem()) {
|
|
1948
|
problem = true;
|
|
1949
|
}
|
|
1950
|
}
|
|
1951
|
else if (state.getDataHolder().nomenclatureCode.toString().equals("Botanical") || state.getDataHolder().nomenclatureCode.toString().contains("ICBN")) {
|
|
1952
|
taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, null);
|
|
1953
|
if (taxonName.hasProblem()) {
|
|
1954
|
problem = true;
|
|
1955
|
}
|
|
1956
|
}
|
|
1957
|
else if (state.getDataHolder().nomenclatureCode.toString().equals("Bacterial") || state.getDataHolder().nomenclatureCode.toString().contains("ICBN")) {
|
|
1958
|
taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, null);
|
|
1959
|
if (taxonName.hasProblem()) {
|
|
1960
|
problem = true;
|
|
1961
|
}
|
|
1962
|
}
|
|
1963
|
else if (state.getDataHolder().nomenclatureCode.toString().equals("Cultivar") || state.getDataHolder().nomenclatureCode.toString().contains("ICNCP")) {
|
|
1964
|
taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, null);
|
|
1965
|
if (taxonName.hasProblem()) {
|
|
1966
|
problem = true;
|
|
1967
|
}
|
|
1968
|
}
|
|
1969
|
if (problem) {
|
|
1970
|
String message = String.format("Parsing problems for %s", scientificName);
|
|
1971
|
if(taxonName!=null){
|
|
1972
|
for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
|
|
1973
|
message += "\n\t- "+parserProblem;
|
|
1974
|
}
|
|
1975
|
}
|
|
1976
|
report.addInfoMessage(message);
|
|
1977
|
logger.info(message);
|
|
1978
|
}
|
|
1979
|
return taxonName;
|
|
1980
|
|
|
1981
|
}
|
|
1982
|
|
|
1983
|
/**
|
|
1984
|
* Create the name without automatic parsing, either because it failed, or because the user deactivated it.
|
|
1985
|
* The name is built upon the ABCD fields
|
|
1986
|
* @param atomisedMap : the ABCD atomised fields
|
|
1987
|
* @param fullName : the full scientific name
|
|
1988
|
* @param state
|
|
1989
|
* @return the corresponding Botanical or Zoological or... name
|
|
1990
|
*/
|
|
1991
|
private NonViralName<?> setTaxonNameByType(
|
|
1992
|
HashMap<String, String> atomisedMap, String fullName, Abcd206ImportState state) {
|
|
1993
|
boolean problem = false;
|
|
1994
|
if(DEBUG) {
|
|
1995
|
logger.info("settaxonnamebytype " + state.getDataHolder().nomenclatureCode.toString());
|
|
1996
|
}
|
|
1997
|
|
|
1998
|
if (state.getDataHolder().nomenclatureCode.equals("Zoological")) {
|
|
1999
|
NonViralName<ZoologicalName> taxonName = ZoologicalName.NewInstance(null);
|
|
2000
|
taxonName.setFullTitleCache(fullName, true);
|
|
2001
|
taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
|
|
2002
|
taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
|
|
2003
|
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
|
|
2004
|
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
|
|
2005
|
|
|
2006
|
if (taxonName.getGenusOrUninomial() != null){
|
|
2007
|
taxonName.setRank(Rank.GENUS());
|
|
2008
|
}
|
|
2009
|
|
|
2010
|
if (taxonName.getInfraGenericEpithet() != null){
|
|
2011
|
taxonName.setRank(Rank.SUBGENUS());
|
|
2012
|
}
|
|
2013
|
|
|
2014
|
if (taxonName.getSpecificEpithet() != null){
|
|
2015
|
taxonName.setRank(Rank.SPECIES());
|
|
2016
|
}
|
|
2017
|
|
|
2018
|
if (taxonName.getInfraSpecificEpithet() != null){
|
|
2019
|
taxonName.setRank(Rank.SUBSPECIES());
|
|
2020
|
}
|
|
2021
|
|
|
2022
|
Team team = null;
|
|
2023
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
2024
|
team = Team.NewInstance();
|
|
2025
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
|
|
2026
|
}
|
|
2027
|
else {
|
|
2028
|
if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
|
|
2029
|
team = Team.NewInstance();
|
|
2030
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
|
|
2031
|
}
|
|
2032
|
}
|
|
2033
|
if (team != null) {
|
|
2034
|
taxonName.setBasionymAuthorship(team);
|
|
2035
|
}
|
|
2036
|
else {
|
|
2037
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
2038
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
|
|
2039
|
}
|
|
2040
|
else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
|
|
2041
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
|
|
2042
|
}
|
|
2043
|
}
|
|
2044
|
if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
|
|
2045
|
team = Team.NewInstance();
|
|
2046
|
team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
|
|
2047
|
taxonName.setCombinationAuthorship(team);
|
|
2048
|
}
|
|
2049
|
if (taxonName.hasProblem()) {
|
|
2050
|
logger.info("pb ICZN");
|
|
2051
|
problem = true;
|
|
2052
|
}
|
|
2053
|
else {
|
|
2054
|
return taxonName;
|
|
2055
|
}
|
|
2056
|
}
|
|
2057
|
else if (state.getDataHolder().nomenclatureCode.equals("Botanical")) {
|
|
2058
|
BotanicalName taxonName = (BotanicalName) parseScientificName(fullName, state, report);
|
|
2059
|
if (taxonName != null){
|
|
2060
|
return taxonName;
|
|
2061
|
}
|
|
2062
|
else{
|
|
2063
|
taxonName = BotanicalName.NewInstance(null);
|
|
2064
|
}
|
|
2065
|
taxonName.setFullTitleCache(fullName, true);
|
|
2066
|
taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
|
|
2067
|
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
|
|
2068
|
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
|
|
2069
|
try {
|
|
2070
|
taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
|
|
2071
|
} catch (Exception e) {
|
|
2072
|
if (taxonName.getInfraSpecificEpithet() != null){
|
|
2073
|
taxonName.setRank(Rank.SUBSPECIES());
|
|
2074
|
}
|
|
2075
|
else if (taxonName.getSpecificEpithet() != null){
|
|
2076
|
taxonName.setRank(Rank.SPECIES());
|
|
2077
|
}
|
|
2078
|
else if (taxonName.getInfraGenericEpithet() != null){
|
|
2079
|
taxonName.setRank(Rank.SUBGENUS());
|
|
2080
|
}
|
|
2081
|
else if (taxonName.getGenusOrUninomial() != null){
|
|
2082
|
taxonName.setRank(Rank.GENUS());
|
|
2083
|
}
|
|
2084
|
}
|
|
2085
|
Team team = null;
|
|
2086
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
2087
|
team = Team.NewInstance();
|
|
2088
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
|
|
2089
|
taxonName.setBasionymAuthorship(team);
|
|
2090
|
}
|
|
2091
|
if (getFromMap(atomisedMap, "AuthorTeam") != null) {
|
|
2092
|
team = Team.NewInstance();
|
|
2093
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
|
|
2094
|
taxonName.setCombinationAuthorship(team);
|
|
2095
|
}
|
|
2096
|
if (team == null) {
|
|
2097
|
if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
|
|
2098
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
|
|
2099
|
}
|
|
2100
|
else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
|
|
2101
|
taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
|
|
2102
|
}
|
|
2103
|
}
|
|
2104
|
if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
|
|
2105
|
team = Team.NewInstance();
|
|
2106
|
team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
|
|
2107
|
taxonName.setCombinationAuthorship(team);
|
|
2108
|
}
|
|
2109
|
if (taxonName.hasProblem()) {
|
|
2110
|
logger.info("pb ICBN");
|
|
2111
|
problem = true;
|
|
2112
|
}
|
|
2113
|
else {
|
|
2114
|
return taxonName;
|
|
2115
|
}
|
|
2116
|
}
|
|
2117
|
else if (state.getDataHolder().nomenclatureCode.equals("Bacterial")) {
|
|
2118
|
NonViralName<BacterialName> taxonName = BacterialName.NewInstance(null);
|
|
2119
|
taxonName.setFullTitleCache(fullName, true);
|
|
2120
|
taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
|
|
2121
|
taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
|
|
2122
|
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
|
|
2123
|
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
|
|
2124
|
|
|
2125
|
if (taxonName.getGenusOrUninomial() != null){
|
|
2126
|
taxonName.setRank(Rank.GENUS());
|
|
2127
|
}
|
|
2128
|
else if (taxonName.getInfraGenericEpithet() != null){
|
|
2129
|
taxonName.setRank(Rank.SUBGENUS());
|
|
2130
|
}
|
|
2131
|
else if (taxonName.getSpecificEpithet() != null){
|
|
2132
|
taxonName.setRank(Rank.SPECIES());
|
|
2133
|
}
|
|
2134
|
else if (taxonName.getInfraSpecificEpithet() != null){
|
|
2135
|
taxonName.setRank(Rank.SUBSPECIES());
|
|
2136
|
}
|
|
2137
|
|
|
2138
|
if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
|
|
2139
|
Team team = Team.NewInstance();
|
|
2140
|
team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
|
|
2141
|
taxonName.setCombinationAuthorship(team);
|
|
2142
|
}
|
|
2143
|
if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
|
|
2144
|
Team team = Team.NewInstance();
|
|
2145
|
team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
|
|
2146
|
taxonName.setBasionymAuthorship(team);
|
|
2147
|
}
|
|
2148
|
if (taxonName.hasProblem()) {
|
|
2149
|
logger.info("pb ICNB");
|
|
2150
|
problem = true;
|
|
2151
|
}
|
|
2152
|
else {
|
|
2153
|
return taxonName;
|
|
2154
|
}
|
|
2155
|
}
|
|
2156
|
else if (state.getDataHolder().nomenclatureCode.equals("Cultivar")) {
|
|
2157
|
CultivarPlantName taxonName = CultivarPlantName.NewInstance(null);
|
|
2158
|
|
|
2159
|
if (taxonName.hasProblem()) {
|
|
2160
|
logger.info("pb ICNCP");
|
|
2161
|
problem = true;
|
|
2162
|
}
|
|
2163
|
else {
|
|
2164
|
return taxonName;
|
|
2165
|
}
|
|
2166
|
return taxonName;
|
|
2167
|
}
|
|
2168
|
|
|
2169
|
if (problem) {
|
|
2170
|
logger.info("Problem im setTaxonNameByType ");
|
|
2171
|
NonViralName<?> taxonName = NonViralName.NewInstance(null);
|
|
2172
|
taxonName.setFullTitleCache(fullName, true);
|
|
2173
|
return taxonName;
|
|
2174
|
}
|
|
2175
|
NonViralName<?> tn = NonViralName.NewInstance(null);
|
|
2176
|
return tn;
|
|
2177
|
}
|
|
2178
|
|
|
2179
|
|
|
2180
|
/**
|
|
2181
|
* Get a formated string from a hashmap
|
|
2182
|
* @param atomisedMap
|
|
2183
|
* @param key
|
|
2184
|
* @return
|
|
2185
|
*/
|
|
2186
|
private String getFromMap(HashMap<String, String> atomisedMap, String key) {
|
|
2187
|
String value = null;
|
|
2188
|
if (atomisedMap.containsKey(key)) {
|
|
2189
|
value = atomisedMap.get(key);
|
|
2190
|
}
|
|
2191
|
|
|
2192
|
try {
|
|
2193
|
if (value != null && key.matches(".*Year.*")) {
|
|
2194
|
value = value.trim();
|
|
2195
|
if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
|
|
2196
|
String tmp = value.split("[0-9]{4}$")[0];
|
|
2197
|
int year = Integer.parseInt(value.split(tmp)[1]);
|
|
2198
|
if (year >= 1752) {
|
|
2199
|
value = tmp;
|
|
2200
|
}
|
|
2201
|
else {
|
|
2202
|
value = null;
|
|
2203
|
}
|
|
2204
|
}
|
|
2205
|
else {
|
|
2206
|
value = null;
|
|
2207
|
}
|
|
2208
|
}
|
|
2209
|
}
|
|
2210
|
catch (Exception e) {
|
|
2211
|
value = null;
|
|
2212
|
}
|
|
2213
|
return value;
|
|
2214
|
}
|
|
2215
|
|
|
2216
|
// private void compareABCDtoCDM(URI urlFileName, List<String> knownElts, Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
2217
|
// try {
|
|
2218
|
// DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
|
|
2219
|
// DocumentBuilder constructeur = factory.newDocumentBuilder();
|
|
2220
|
// URL url = urlFileName.toURL();
|
|
2221
|
// Object o = url.getContent();
|
|
2222
|
// InputStream is = (InputStream) o;
|
|
2223
|
// Document document = constructeur.parse(is);
|
|
2224
|
// Element root = document.getDocumentElement();
|
|
2225
|
// abcdFieldGetter.traverse(root);
|
|
2226
|
// }
|
|
2227
|
// catch (ParserConfigurationException e){
|
|
2228
|
// e.printStackTrace();
|
|
2229
|
// }
|
|
2230
|
// catch (SAXException e) {
|
|
2231
|
// e.printStackTrace();
|
|
2232
|
// }
|
|
2233
|
// catch (IOException e) {
|
|
2234
|
// e.printStackTrace();
|
|
2235
|
// }
|
|
2236
|
// Set<String> elts = state.getDataHolder().allABCDelements.keySet();
|
|
2237
|
// Iterator<String> it = elts.iterator();
|
|
2238
|
// String elt;
|
|
2239
|
// while (it.hasNext()) {
|
|
2240
|
// elt = it.next();
|
|
2241
|
// if (knownElts.indexOf(elt) == -1) {
|
|
2242
|
// if(DEBUG) {
|
|
2243
|
// logger.info("Unmerged ABCD element: " + elt + " - "+ state.getDataHolder().allABCDelements.get(elt));
|
|
2244
|
// }
|
|
2245
|
// }
|
|
2246
|
// }
|
|
2247
|
// }
|
|
2248
|
|
|
2249
|
/**
|
|
2250
|
* Load the list of names from the ABCD file and save them
|
|
2251
|
* @param state : the current ABCD import state
|
|
2252
|
* @param unitsList : the unit list from the ABCD file
|
|
2253
|
* @param abcdFieldGetter : the ABCD parser
|
|
2254
|
*/
|
|
2255
|
private void prepareCollectors(Abcd206ImportState state, NodeList unitsList, Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
2256
|
List<String> collectors = new ArrayList<String>();
|
|
2257
|
List<String> teams = new ArrayList<String>();
|
|
2258
|
List<List<String>> collectorinteams = new ArrayList<List<String>>();
|
|
2259
|
|
|
2260
|
for (int i = 0; i < unitsList.getLength(); i++) {
|
|
2261
|
this.getCollectorsFromXML((Element) unitsList.item(i), abcdFieldGetter, state);
|
|
2262
|
for (String agent : state.getDataHolder().gatheringAgentList) {
|
|
2263
|
collectors.add(agent);
|
|
2264
|
}
|
|
2265
|
List<String> tmpTeam = new ArrayList<String>(new HashSet<String>(state.getDataHolder().gatheringTeamList));
|
|
2266
|
if(!tmpTeam.isEmpty()) {
|
|
2267
|
teams.add(StringUtils.join(tmpTeam.toArray()," & "));
|
|
2268
|
}
|
|
2269
|
for (String agent:tmpTeam) {
|
|
2270
|
collectors.add(agent);
|
|
2271
|
}
|
|
2272
|
}
|
|
2273
|
|
|
2274
|
List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
|
|
2275
|
List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
|
|
2276
|
|
|
2277
|
|
|
2278
|
//existing teams in DB
|
|
2279
|
Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
|
|
2280
|
List<UuidAndTitleCache<Team>> hiberTeam = getAgentService().getTeamUuidAndTitleCache();
|
|
2281
|
|
|
2282
|
Set<UUID> uuids = new HashSet<UUID>();
|
|
2283
|
for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
|
|
2284
|
uuids.add(hibernateT.getUuid());
|
|
2285
|
}
|
|
2286
|
if (!uuids.isEmpty()){
|
|
2287
|
List<AgentBase> existingTeams = getAgentService().find(uuids);
|
|
2288
|
for (AgentBase<?> existingP:existingTeams){
|
|
2289
|
titleCacheTeam.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Team.class));
|
|
2290
|
}
|
|
2291
|
}
|
|
2292
|
|
|
2293
|
|
|
2294
|
Map<String,UUID> teamMap = new HashMap<String, UUID>();
|
|
2295
|
for (UuidAndTitleCache<Team> uuidt:hiberTeam){
|
|
2296
|
teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
|
|
2297
|
}
|
|
2298
|
|
|
2299
|
//existing persons in DB
|
|
2300
|
List<UuidAndTitleCache<Person>> hiberPersons = getAgentService().getPersonUuidAndTitleCache();
|
|
2301
|
Map<String,Person> titleCachePerson = new HashMap<String, Person>();
|
|
2302
|
uuids = new HashSet<UUID>();
|
|
2303
|
for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
2304
|
uuids.add(hibernateP.getUuid());
|
|
2305
|
}
|
|
2306
|
|
|
2307
|
if (!uuids.isEmpty()){
|
|
2308
|
List<AgentBase> existingPersons = getAgentService().find(uuids);
|
|
2309
|
for (AgentBase<?> existingP:existingPersons){
|
|
2310
|
titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Person.class));
|
|
2311
|
}
|
|
2312
|
}
|
|
2313
|
|
|
2314
|
Map<String,UUID> personMap = new HashMap<String, UUID>();
|
|
2315
|
for (UuidAndTitleCache<Person> person:hiberPersons){
|
|
2316
|
personMap.put(person.getTitleCache(), person.getUuid());
|
|
2317
|
}
|
|
2318
|
|
|
2319
|
java.util.Collection<Person> personToadd = new ArrayList<Person>();
|
|
2320
|
java.util.Collection<Team> teamToAdd = new ArrayList<Team>();
|
|
2321
|
|
|
2322
|
for (String collector:collectorsU){
|
|
2323
|
Person p = Person.NewInstance();
|
|
2324
|
p.setTitleCache(collector,true);
|
|
2325
|
if (!personMap.containsKey(p.getTitleCache())){
|
|
2326
|
personToadd.add(p);
|
|
2327
|
}
|
|
2328
|
}
|
|
2329
|
for (String team:teamsU){
|
|
2330
|
Team p = Team.NewInstance();
|
|
2331
|
p.setTitleCache(team,true);
|
|
2332
|
if (!teamMap.containsKey(p.getTitleCache())){
|
|
2333
|
teamToAdd.add(p);
|
|
2334
|
}
|
|
2335
|
}
|
|
2336
|
|
|
2337
|
if(!personToadd.isEmpty()){
|
|
2338
|
for (Person agent: personToadd){
|
|
2339
|
save(agent, state);
|
|
2340
|
titleCachePerson.put(agent.getTitleCache(),CdmBase.deproxy(agent, Person.class) );
|
|
2341
|
}
|
|
2342
|
}
|
|
2343
|
|
|
2344
|
Person ptmp ;
|
|
2345
|
Map <String,Integer>teamdone = new HashMap<String, Integer>();
|
|
2346
|
for (List<String> collteam: collectorinteams){
|
|
2347
|
if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
|
|
2348
|
Team team = new Team();
|
|
2349
|
boolean em =true;
|
|
2350
|
for (String collector:collteam){
|
|
2351
|
ptmp = Person.NewInstance();
|
|
2352
|
ptmp.setTitleCache(collector,true);
|
|
2353
|
Person p2 = titleCachePerson.get(ptmp.getTitleCache());
|
|
2354
|
team.addTeamMember(p2);
|
|
2355
|
em=false;
|
|
2356
|
}
|
|
2357
|
if (!em) {
|
|
2358
|
teamToAdd.add(team);
|
|
2359
|
}
|
|
2360
|
teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
|
|
2361
|
}
|
|
2362
|
}
|
|
2363
|
|
|
2364
|
if(!teamToAdd.isEmpty()){
|
|
2365
|
for (Team agent: teamToAdd){
|
|
2366
|
save(agent, state);
|
|
2367
|
titleCacheTeam.put(agent.getTitleCache(), CdmBase.deproxy( agent,Team.class) );
|
|
2368
|
}
|
|
2369
|
}
|
|
2370
|
|
|
2371
|
state.getConfig().setTeams(titleCacheTeam);
|
|
2372
|
state.getConfig().setPersons(titleCachePerson);
|
|
2373
|
}
|
|
2374
|
|
|
2375
|
@Override
|
|
2376
|
protected boolean isIgnore(Abcd206ImportState state) {
|
|
2377
|
return false;
|
|
2378
|
}
|
|
2379
|
|
|
2380
|
@Override
|
|
2381
|
public byte[] getByteArray() {
|
|
2382
|
ByteArrayOutputStream importStream = new ByteArrayOutputStream();
|
|
2383
|
report.printReport(new PrintStream(importStream));
|
|
2384
|
return importStream.toByteArray();
|
|
2385
|
}
|
|
2386
|
|
|
2387
|
}
|