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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.InputStream;
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import java.net.MalformedURLException;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import 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.ICdmRepository;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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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.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.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.Annotation;
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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.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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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.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.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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/**
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* @author p.kelbert
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* @author p.plitzner
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* @author k.luther
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* @since 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 long serialVersionUID = 3918095362150986307L;
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private static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
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private static final Logger logger = Logger.getLogger(Abcd206Import.class);
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public Abcd206Import() {
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super();
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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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Abcd206ImportConfigurator config = state.getConfig();
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Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
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MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
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state.setPersonStore(authorStore);
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MapWrapper<Reference> referenceStore = (MapWrapper<Reference>)stores.get(ICdmIO.REFERENCE_STORE);
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createKindOfUnitsMap(state);
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URI sourceUri = config.getSourceUri();
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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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InputStream response = null;
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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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if (config.getOccurenceQuery() != null){
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BioCaseQueryServiceWrapper queryService = new BioCaseQueryServiceWrapper();
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try {
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response = queryService.query(config.getOccurenceQuery(), sourceUri);
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state.setActualAccessPoint(sourceUri);
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}catch(Exception e){
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logger.error("An error during ABCD import");
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}
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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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// List<Reference> references = new ArrayList<Reference>();
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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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//
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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 : referenceStore.getAllValues()) {
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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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if (state.getConfig().getSourceReference() != null){
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state.setRef(state.getConfig().getSourceReference());
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}else{
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state.setRef(ReferenceFactory.newGeneric());
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state.getRef().setUri(sourceUri);
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state.getRef().setTitle(StringUtils.substringAfter(sourceUri.toString(), "dsa="));
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if (!StringUtils.isBlank(state.getConfig().getSourceReferenceTitle())){
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state.getRef().setTitle(state.getConfig().getSourceReferenceTitle());
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}
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}
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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<>();
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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.getTitleCache().equalsIgnoreCase(name)) {
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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(false), 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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if (response == null){
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response =state.getConfig().getSource();
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}
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UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(response, state.getReport());
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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() + 3);
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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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if (config.getNomenclaturalCode() != null){
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state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().getKey());
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}
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prepareCollectors(state, unitsList, abcdFieldGetter);
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// save authors
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getAgentService().saveOrUpdate((java.util.Collection)state.getPersonStore().objects());
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commitTransaction(state.getTx());
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state.setTx(startTransaction());
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if (state.getDefaultClassification(false) != null){
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state.setDefaultClassification(getClassificationService().load(state.getDefaultClassification(false).getUuid()));
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}
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if (state.getClassification() != null){
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state.setClassification(getClassificationService().load(state.getClassification().getUuid()));
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}
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state.setAssociationRefs(new ArrayList<>());
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state.setDescriptionRefs(new ArrayList<>());
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state.setDerivedUnitSources(new ArrayList<>());
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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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Abcd206ImportParser.setUnitPropertiesXML( item, abcdFieldGetter, state);
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updateProgress(state, "Importing data for unit "+state.getDataHolder().getUnitID()+" ("+i+"/"+unitsList.getLength()+")");
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//import unit + field unit data
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state.setAssociatedUnitIds(state.getDataHolder().getAssociatedUnitIds());
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this.handleSingleUnit(state, item, true);
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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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state.getReport().addException(errorDuringImport, e);
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}
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finally{
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state.getReport().printReport(state.getConfig().getReportUri());
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}
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if (state.getConfig().isDownloadSequenceData()){
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//download fasta files for imported sequences
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//TODO: where to store the files and how to create the new Blast DB
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}
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return;
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}
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/**
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*
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*/
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private void createKindOfUnitsMap(Abcd206ImportState state) {
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ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
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if (cdmRepository == null){
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cdmRepository = this;
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}
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List<DefinedTerm> terms = cdmRepository.getTermService().listByTermType(TermType.KindOfUnit, null, 0, null, null);
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kindOfUnitsMap = new HashMap<>();
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for (DefinedTerm kindOfUnit:terms) {
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kindOfUnitsMap.put(kindOfUnit.getLabel().toLowerCase(), kindOfUnit);
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}
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}
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/**
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* @param state
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* @param item
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*/
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private void getSiblings(Abcd206ImportState state, Object item, DerivedUnitFacade facade) {
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String unitId = facade.getCatalogNumber();
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323
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if (unitId == null){
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unitId = facade.getAccessionNumber();
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}
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UnitAssociationParser unitParser = new UnitAssociationParser(state.getPrefix(), state.getReport(), state.getCdmRepository());
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UnitAssociationWrapper unitAssociationWrapper = null;
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for (URI accessPoint: state.getActualAccesPoint()){
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unitAssociationWrapper = unitParser.parseSiblings(unitId, accessPoint);
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if (unitAssociationWrapper != null && unitAssociationWrapper.getAssociatedUnits() != null){
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break;
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}
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}
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DerivedUnit currentUnit = state.getDerivedUnitBase();
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// DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
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FieldUnit currentFieldUnit = facade.getFieldUnit(false);
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if(unitAssociationWrapper!=null){
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NodeList associatedUnits = unitAssociationWrapper.getAssociatedUnits();
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341
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if(associatedUnits!=null){
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342
|
for(int m=0;m<associatedUnits.getLength();m++){
|
|
343
|
if(associatedUnits.item(m) instanceof Element){
|
|
344
|
state.reset();
|
|
345
|
String associationType = AbcdParseUtility.parseFirstTextContent(((Element) associatedUnits.item(m)).getElementsByTagName(state.getPrefix()+"AssociationType"));
|
|
346
|
|
|
347
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), unitAssociationWrapper.getPrefix()), state);
|
|
348
|
// logger.debug("derived unit: " + state.getDerivedUnitBase().toString() + " associated unit: " +state.getDataHolder().getKindOfUnit() + ", " + state.getDataHolder().accessionNumber + ", " + state.getDataHolder().getRecordBasis() + ", " + state.getDataHolder().getUnitID());
|
|
349
|
|
|
350
|
handleSingleUnit(state, associatedUnits.item(m), false);
|
|
351
|
|
|
352
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
353
|
FieldUnit associatedFieldUnit = null;
|
|
354
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid(), null);
|
|
355
|
//ignore field unit if associated unit has more than one
|
|
356
|
if(associatedFieldUnits.size()>1){
|
|
357
|
state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
358
|
}
|
|
359
|
else if(associatedFieldUnits.size()==1){
|
|
360
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
361
|
}
|
|
362
|
//parent-child relation:
|
|
363
|
if(associationType.contains("individual") || associationType.contains("culture") || associationType.contains("sample")){
|
|
364
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(currentUnit, associatedUnit, DerivationEventType.ACCESSIONING());
|
|
365
|
if(associatedFieldUnit!=null && associatedFieldUnit != currentFieldUnit){
|
|
366
|
associatedFieldUnit.removeDerivationEvent(updatedDerivationEvent);
|
|
367
|
state.getCdmRepository().getOccurrenceService().delete(associatedFieldUnit);
|
|
368
|
}
|
|
369
|
state.getReport().addDerivate(associatedUnit, currentUnit, state.getConfig());
|
|
370
|
}
|
|
371
|
save(associatedUnit, state);
|
|
372
|
|
|
373
|
}
|
|
374
|
}
|
|
375
|
}
|
|
376
|
}
|
|
377
|
state.reset();
|
|
378
|
state.setDerivedUnitBase(currentUnit);
|
|
379
|
|
|
380
|
}
|
|
381
|
|
|
382
|
/**
|
|
383
|
* Handle a single unit
|
|
384
|
* @param state
|
|
385
|
* @param item
|
|
386
|
*/
|
|
387
|
@Override
|
|
388
|
public void handleSingleUnit(Abcd206ImportState state, Object itemObject){
|
|
389
|
handleSingleUnit(state, itemObject, true);
|
|
390
|
}
|
|
391
|
|
|
392
|
|
|
393
|
@SuppressWarnings("rawtypes")
|
|
394
|
public void handleSingleUnit(Abcd206ImportState state, Object itemObject, boolean handleAssociatedUnits) {
|
|
395
|
Element item = (Element) itemObject;
|
|
396
|
|
|
397
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
398
|
if (logger.isDebugEnabled()) {
|
|
399
|
logger.info("handleSingleUnit "+state.getRef());
|
|
400
|
}
|
|
401
|
try {
|
|
402
|
ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
|
|
403
|
if(cdmAppController==null){
|
|
404
|
cdmAppController = this;
|
|
405
|
}
|
|
406
|
//check if unit already exists
|
|
407
|
DerivedUnitFacade derivedUnitFacade = null;
|
|
408
|
if(state.getConfig().isIgnoreImportOfExistingSpecimen()){
|
|
409
|
SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(state.getDataHolder().getUnitID(), state);
|
|
410
|
if(existingSpecimen!=null && existingSpecimen.isInstanceOf(DerivedUnit.class)){
|
|
411
|
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);
|
|
412
|
state.setDerivedUnitBase(derivedUnit);
|
|
413
|
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
|
|
414
|
if (handleAssociatedUnits){
|
|
415
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
416
|
}
|
|
417
|
|
|
418
|
state.getReport().addAlreadyExistingSpecimen(SpecimenImportUtility.getUnitID(derivedUnit, config), derivedUnit);
|
|
419
|
|
|
420
|
return;
|
|
421
|
}
|
|
422
|
}
|
|
423
|
// TODO: implement overwrite/merge specimen
|
|
424
|
// else if(state.getConfig().isOverwriteExistingSpecimens()){
|
|
425
|
// Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
|
|
426
|
// if(!existingSpecimens.getRecords().isEmpty()){
|
|
427
|
// derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit);
|
|
428
|
// derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
|
|
429
|
// fieldUnit = derivedUnitFacade.getFieldUnit(true);
|
|
430
|
// }
|
|
431
|
// }
|
|
432
|
//import new specimen
|
|
433
|
|
|
434
|
// import DNA unit
|
|
435
|
if(state.getDataHolder().getKindOfUnit() !=null && state.getDataHolder().getKindOfUnit().equalsIgnoreCase("dna")){
|
|
436
|
AbcdDnaParser dnaParser = new AbcdDnaParser(state.getPrefix(), state.getReport(), state.getCdmRepository());
|
|
437
|
DnaSample dnaSample = dnaParser.parse(item, state);
|
|
438
|
save(dnaSample, state);
|
|
439
|
//set dna as derived unit to avoid creating an extra specimen for this dna sample (instead just the field unit will be created)
|
|
440
|
state.setDerivedUnitBase(dnaSample);
|
|
441
|
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
|
|
442
|
}
|
|
443
|
else{
|
|
444
|
// create facade
|
|
445
|
derivedUnitFacade = getFacade(state);
|
|
446
|
state.setDerivedUnitBase(derivedUnitFacade.innerDerivedUnit());
|
|
447
|
|
|
448
|
}
|
|
449
|
|
|
450
|
/**
|
|
451
|
* GATHERING EVENT
|
|
452
|
*/
|
|
453
|
|
|
454
|
//look for existing fieldUnit
|
|
455
|
|
|
456
|
FieldUnit fieldUnit = state.getFieldUnit(state.getDataHolder().getFieldNumber());
|
|
457
|
|
|
458
|
|
|
459
|
// gathering event
|
|
460
|
UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(cdmAppController.getTermService(),
|
|
461
|
state.getDataHolder().locality, state.getDataHolder().languageIso, state.getDataHolder().longitude,
|
|
462
|
state.getDataHolder().latitude, state.getDataHolder().getGatheringElevationText(),
|
|
463
|
state.getDataHolder().getGatheringElevationMin(), state.getDataHolder().getGatheringElevationMax(),
|
|
464
|
state.getDataHolder().getGatheringElevationUnit(), state.getDataHolder().getGatheringDateText(),
|
|
465
|
state.getDataHolder().getGatheringNotes(), state.getDataHolder().getGatheringMethod(), state.getTransformer().getReferenceSystemByKey(
|
|
466
|
state.getDataHolder().getGatheringSpatialDatum()),
|
|
467
|
state.getConfig());
|
|
468
|
|
|
469
|
unitsGatheringEvent.setGatheringDepth(state.getDataHolder().getGatheringDepthText(),state.getDataHolder().getGatheringDepthMin(), state.getDataHolder().getGatheringDepthMax(), state.getDataHolder().getGatheringDepthUnit());
|
|
470
|
//unitsGatheringEvent.setHeight(heightText, heightMin, heightMax, heightUnit);
|
|
471
|
if(state.getDataHolder().gatheringAgentsList.isEmpty()) {
|
|
472
|
unitsGatheringEvent.setCollector(state.getPersonStore().get(state.getDataHolder().gatheringAgentsText), config);
|
|
473
|
}else{
|
|
474
|
unitsGatheringEvent.setCollector(state.getPersonStore().get(state.getDataHolder().gatheringAgentsList.toString()), config);
|
|
475
|
}
|
|
476
|
// count
|
|
477
|
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
|
|
478
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());
|
|
479
|
unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, (state.getConfig()), cdmAppController.getTermService(), cdmAppController.getOccurrenceService(), cdmAppController.getVocabularyService());
|
|
480
|
|
|
481
|
DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();
|
|
482
|
|
|
483
|
// other areas
|
|
484
|
unitsGatheringArea = new UnitsGatheringArea();
|
|
485
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());
|
|
486
|
|
|
487
|
unitsGatheringArea.setAreas(state.getDataHolder().getNamedAreaList(),(state.getConfig()), cdmAppController.getTermService(), cdmAppController.getVocabularyService());
|
|
488
|
|
|
489
|
ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
|
|
490
|
for (DefinedTermBase namedArea : nas) {
|
|
491
|
unitsGatheringEvent.addArea(namedArea);
|
|
492
|
}
|
|
493
|
|
|
494
|
// copy gathering event to facade
|
|
495
|
GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
|
|
496
|
if (fieldUnit != null){
|
|
497
|
derivedUnitFacade.setFieldUnit(fieldUnit);
|
|
498
|
}
|
|
499
|
|
|
500
|
derivedUnitFacade.setLocality(gatheringEvent.getLocality());
|
|
501
|
derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
|
|
502
|
derivedUnitFacade.setCollector(gatheringEvent.getCollector());
|
|
503
|
derivedUnitFacade.setCountry((NamedArea)areaCountry);
|
|
504
|
derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());
|
|
505
|
derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());
|
|
506
|
derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());
|
|
507
|
derivedUnitFacade.setDistanceToGroundText(gatheringEvent.getDistanceToGroundText());
|
|
508
|
derivedUnitFacade.setDistanceToGroundMax(gatheringEvent.getDistanceToGroundMax());
|
|
509
|
derivedUnitFacade.setDistanceToGround(gatheringEvent.getDistanceToGround());
|
|
510
|
derivedUnitFacade.setDistanceToWaterSurfaceText(gatheringEvent.getDistanceToWaterSurfaceText());
|
|
511
|
derivedUnitFacade.setDistanceToWaterSurfaceMax(gatheringEvent.getDistanceToWaterSurfaceMax());
|
|
512
|
derivedUnitFacade.setDistanceToWaterSurface(gatheringEvent.getDistanceToWaterSurface());
|
|
513
|
derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
|
|
514
|
derivedUnitFacade.setCollectingMethod(gatheringEvent.getCollectingMethod());
|
|
515
|
|
|
516
|
for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
|
|
517
|
derivedUnitFacade.addCollectingArea((NamedArea) area);
|
|
518
|
}
|
|
519
|
// derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
|
|
520
|
// TODO exsiccatum
|
|
521
|
|
|
522
|
// add fieldNumber
|
|
523
|
derivedUnitFacade.setFieldNumber(NB(state.getDataHolder().getFieldNumber()));
|
|
524
|
save(unitsGatheringEvent.getLocality(), state);
|
|
525
|
|
|
526
|
// add unitNotes
|
|
527
|
if (state.getDataHolder().getUnitNotes() != null){
|
|
528
|
derivedUnitFacade.addAnnotation(Annotation.NewDefaultLanguageInstance(NB(state.getDataHolder().getUnitNotes())));
|
|
529
|
}
|
|
530
|
|
|
531
|
|
|
532
|
|
|
533
|
// //add Multimedia URLs
|
|
534
|
if (state.getDataHolder().getMultimediaObjects().size() != -1) {
|
|
535
|
for (String multimediaObject : state.getDataHolder().getMultimediaObjects().keySet()) {
|
|
536
|
Media media;
|
|
537
|
try {
|
|
538
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
539
|
Map<String, String> attributes = state.getDataHolder().getMultimediaObjects().get(multimediaObject);
|
|
540
|
if (attributes.containsKey("Context")){
|
|
541
|
LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
|
|
542
|
media.addDescription(description);
|
|
543
|
}
|
|
544
|
if (attributes.containsKey("Comment")){
|
|
545
|
LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
|
|
546
|
media.addDescription(description);
|
|
547
|
}
|
|
548
|
if (attributes.containsKey("Creators")){
|
|
549
|
String creators = attributes.get("Creators");
|
|
550
|
Person artist;
|
|
551
|
Team artistTeam;
|
|
552
|
String[] artists;
|
|
553
|
if (creators != null){
|
|
554
|
if (creators.contains("&")){
|
|
555
|
artists = creators.split("&");
|
|
556
|
artistTeam = new Team();
|
|
557
|
for (String creator:artists){
|
|
558
|
artist = Person.NewTitledInstance(creator);
|
|
559
|
artistTeam.addTeamMember(artist);
|
|
560
|
}
|
|
561
|
media.setArtist(artistTeam);
|
|
562
|
} else{
|
|
563
|
|
|
564
|
artist = Person.NewTitledInstance(creators);
|
|
565
|
media.setArtist(artist);
|
|
566
|
}
|
|
567
|
}
|
|
568
|
|
|
569
|
|
|
570
|
|
|
571
|
}
|
|
572
|
|
|
573
|
derivedUnitFacade.addDerivedUnitMedia(media);
|
|
574
|
if(state.getConfig().isAddMediaAsMediaSpecimen()){
|
|
575
|
//add media also as specimen scan
|
|
576
|
MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
|
|
577
|
mediaSpecimen.setMediaSpecimen(media);
|
|
578
|
//do it only once!!
|
|
579
|
DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);
|
|
580
|
if(specimenScanTerm instanceof DefinedTerm){
|
|
581
|
mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
|
|
582
|
}
|
|
583
|
DerivationEvent derivationEvent = DerivationEvent.NewInstance(DerivationEventType.PREPARATION());
|
|
584
|
derivationEvent.addDerivative(mediaSpecimen);
|
|
585
|
derivedUnitFacade.innerDerivedUnit().addDerivationEvent(derivationEvent);
|
|
586
|
}
|
|
587
|
|
|
588
|
} catch (MalformedURLException e) {
|
|
589
|
// TODO Auto-generated catch block
|
|
590
|
e.printStackTrace();
|
|
591
|
}
|
|
592
|
|
|
593
|
}
|
|
594
|
}
|
|
595
|
//multimedia for fieldUnit
|
|
596
|
if (state.getDataHolder().getGatheringMultimediaObjects().size() != -1) {
|
|
597
|
for (String multimediaObject : state.getDataHolder().getGatheringMultimediaObjects().keySet()) {
|
|
598
|
Media media;
|
|
599
|
try {
|
|
600
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
601
|
Map<String, String> attributes = state.getDataHolder().getGatheringMultimediaObjects().get(multimediaObject);
|
|
602
|
if (attributes.containsKey("Context")){
|
|
603
|
LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
|
|
604
|
media.addDescription(description);
|
|
605
|
}
|
|
606
|
if (attributes.containsKey("Comment")){
|
|
607
|
LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
|
|
608
|
media.addDescription(description);
|
|
609
|
}
|
|
610
|
if (attributes.containsKey("Creators")){
|
|
611
|
String creators = attributes.get("Creators");
|
|
612
|
Person artist;
|
|
613
|
Team artistTeam;
|
|
614
|
String[] artists;
|
|
615
|
if (creators != null){
|
|
616
|
if (creators.contains("&")){
|
|
617
|
artists = creators.split("&");
|
|
618
|
artistTeam = new Team();
|
|
619
|
for (String creator:artists){
|
|
620
|
artist = Person.NewTitledInstance(creator);
|
|
621
|
artistTeam.addTeamMember(artist);
|
|
622
|
}
|
|
623
|
media.setArtist(artistTeam);
|
|
624
|
} else{
|
|
625
|
|
|
626
|
artist = Person.NewTitledInstance(creators);
|
|
627
|
media.setArtist(artist);
|
|
628
|
}
|
|
629
|
}
|
|
630
|
|
|
631
|
|
|
632
|
|
|
633
|
}
|
|
634
|
|
|
635
|
derivedUnitFacade.addFieldObjectMedia(media);
|
|
636
|
|
|
637
|
|
|
638
|
} catch (MalformedURLException e) {
|
|
639
|
// TODO Auto-generated catch block
|
|
640
|
e.printStackTrace();
|
|
641
|
}
|
|
642
|
|
|
643
|
}
|
|
644
|
}
|
|
645
|
|
|
646
|
// /*
|
|
647
|
// * merge AND STORE DATA
|
|
648
|
// */
|
|
649
|
// getTermService().saveOrUpdate(areaCountry);// TODO save area sooner
|
|
650
|
//
|
|
651
|
// for (NamedArea area : otherAreas) {
|
|
652
|
// getTermService().saveOrUpdate(area);// merge it sooner (foreach area)
|
|
653
|
// }
|
|
654
|
// save(derivedUnitFacade.getFieldUnit(false), state);
|
|
655
|
if (derivedUnitFacade.getFieldUnit(false) != null){
|
|
656
|
state.setFieldUnit(derivedUnitFacade.getFieldUnit(false));
|
|
657
|
}
|
|
658
|
|
|
659
|
// handle collection data
|
|
660
|
setCollectionData(state, derivedUnitFacade);
|
|
661
|
|
|
662
|
//Reference stuff
|
|
663
|
SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
|
|
664
|
Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<>();
|
|
665
|
|
|
666
|
state.getDataHolder().setDocSources(new ArrayList<>());
|
|
667
|
for (String[] fullReference : state.getDataHolder().getReferenceList()) {
|
|
668
|
String strReference=fullReference[0];
|
|
669
|
String citationDetail = fullReference[1];
|
|
670
|
String citationURL = fullReference[2];
|
|
671
|
|
|
672
|
if (!citationURL.isEmpty()) {
|
|
673
|
citationDetail+=", "+citationURL;
|
|
674
|
}
|
|
675
|
|
|
676
|
Reference reference;
|
|
677
|
if(strReference.equals(state.getRef().getTitleCache())){
|
|
678
|
reference = state.getRef();
|
|
679
|
}
|
|
680
|
else{
|
|
681
|
reference = ReferenceFactory.newGeneric();
|
|
682
|
reference.setTitle(strReference);
|
|
683
|
}
|
|
684
|
|
|
685
|
|
|
686
|
save(reference, state);
|
|
687
|
IdentifiableSource sour = getIdentifiableSource(reference, citationDetail);
|
|
688
|
sour.getCitation().setUri(state.getActualAccessPoint());
|
|
689
|
sour.setType(OriginalSourceType.PrimaryTaxonomicSource);
|
|
690
|
try{
|
|
691
|
if (sour.getCitation() != null){
|
|
692
|
if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {
|
|
693
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());
|
|
694
|
} else {
|
|
695
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache());
|
|
696
|
}
|
|
697
|
}
|
|
698
|
}catch(Exception e){
|
|
699
|
logger.warn("oups");
|
|
700
|
}
|
|
701
|
derivedUnitFacade.addSource(sour);
|
|
702
|
|
|
703
|
}
|
|
704
|
// List<IdentifiableSource> issTmp = new ArrayList<IdentifiableSource>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
705
|
// List<DescriptionElementSource> issTmp2 = new ArrayList<DescriptionElementSource>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
706
|
//
|
|
707
|
// Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
|
|
708
|
// if(issTmp2!=null) {
|
|
709
|
// osbSet.addAll(issTmp2);
|
|
710
|
// }
|
|
711
|
// if(issTmp!=null) {
|
|
712
|
// osbSet.addAll(issTmp);
|
|
713
|
// }
|
|
714
|
|
|
715
|
IdentifiableSource sour = getIdentifiableSource(state.getRef(),null);
|
|
716
|
String idInSource = derivedUnitFacade.getAccessionNumber() != null? derivedUnitFacade.getAccessionNumber():derivedUnitFacade.getCatalogNumber();
|
|
717
|
sour.getCitation().setUri(state.getActualAccessPoint());
|
|
718
|
sour.setIdInSource(idInSource);
|
|
719
|
try{
|
|
720
|
if (sour.getCitation() != null){
|
|
721
|
if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {
|
|
722
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());
|
|
723
|
} else {
|
|
724
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache());
|
|
725
|
}
|
|
726
|
}
|
|
727
|
}catch(Exception e){
|
|
728
|
logger.warn("oups");
|
|
729
|
}
|
|
730
|
|
|
731
|
derivedUnitFacade.addSource(sour);
|
|
732
|
// sourceMap.put(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference(),sour);
|
|
733
|
|
|
734
|
// if( state.getConfig().isInteractWithUser()){
|
|
735
|
// List<OriginalSourceBase<?>>sources=null;
|
|
736
|
// if(!state.isDerivedUnitSourcesSet()){
|
|
737
|
// sources= sui.askForSource(sourceMap, "the unit itself","",getReferenceService(), state.getDataHolder().getDocSources());
|
|
738
|
// state.setDerivedUnitSources(sources);
|
|
739
|
// state.setDerivedUnitSourcesSet(true);
|
|
740
|
// }
|
|
741
|
// else{
|
|
742
|
// sources=state.getDerivedUnitSources();
|
|
743
|
// }
|
|
744
|
//// for (OriginalSourceBase<?> source:sources){
|
|
745
|
//// if(source.isInstanceOf(IdentifiableSource.class)){
|
|
746
|
//// if(sourceNotLinkedToElement(derivedUnitFacade,source)) {
|
|
747
|
//// derivedUnitFacade.addSource((IdentifiableSource)source.clone());
|
|
748
|
//// }
|
|
749
|
//// }else{
|
|
750
|
//// if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {
|
|
751
|
//// derivedUnitFacade.addSource(OriginalSourceType.Import,source.getCitation(),source.getCitationMicroReference(), ioName);
|
|
752
|
//// }
|
|
753
|
//// }
|
|
754
|
//// }
|
|
755
|
// }else{
|
|
756
|
// for (OriginalSourceBase<?> sr : sourceMap.values()){
|
|
757
|
// if(sr.isInstanceOf(IdentifiableSource.class)){
|
|
758
|
// if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
|
|
759
|
// derivedUnitFacade.addSource((IdentifiableSource)sr.clone());
|
|
760
|
// }
|
|
761
|
// }else{
|
|
762
|
// if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
|
|
763
|
// derivedUnitFacade.addSource(OriginalSourceType.Import,sr.getCitation(),sr.getCitationMicroReference(), ioName);
|
|
764
|
// }
|
|
765
|
// }
|
|
766
|
// }
|
|
767
|
// }
|
|
768
|
|
|
769
|
save(state.getDerivedUnitBase(), state);
|
|
770
|
|
|
771
|
if(logger.isDebugEnabled()) {
|
|
772
|
logger.info("saved ABCD specimen ...");
|
|
773
|
}
|
|
774
|
|
|
775
|
// handle identifications
|
|
776
|
handleIdentifications(state, derivedUnitFacade);
|
|
777
|
|
|
778
|
//associatedUnits
|
|
779
|
if (handleAssociatedUnits){
|
|
780
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
781
|
}
|
|
782
|
//siblings/ other children
|
|
783
|
if (derivedUnitFacade.getType() != null && (derivedUnitFacade.getType().equals(SpecimenOrObservationType.LivingSpecimen) || derivedUnitFacade.getType().equals(SpecimenOrObservationType.TissueSample) || derivedUnitFacade.getType().equals(SpecimenOrObservationType.OtherSpecimen)) &&state.getConfig().isGetSiblings()){
|
|
784
|
getSiblings(state, item, derivedUnitFacade);
|
|
785
|
}
|
|
786
|
|
|
787
|
|
|
788
|
} catch (Exception e) {
|
|
789
|
String message = "Error when reading record!";
|
|
790
|
logger.warn(message);
|
|
791
|
state.getReport().addException(message, e);
|
|
792
|
e.printStackTrace();
|
|
793
|
state.setUnsuccessfull();
|
|
794
|
}
|
|
795
|
|
|
796
|
return;
|
|
797
|
}
|
|
798
|
|
|
799
|
@Override
|
|
800
|
protected void importAssociatedUnits(Abcd206ImportState state, Object itemObject, DerivedUnitFacade derivedUnitFacade) {
|
|
801
|
|
|
802
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
803
|
//import associated units
|
|
804
|
FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();
|
|
805
|
//TODO: push state (think of implementing stack architecture for state
|
|
806
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
807
|
DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
808
|
URI currentAccessPoint = state.getActualAccessPoint();
|
|
809
|
String currentPrefix = state.getPrefix();
|
|
810
|
Element item = null;
|
|
811
|
if (itemObject instanceof Element){
|
|
812
|
item = (Element)itemObject;
|
|
813
|
}
|
|
814
|
NodeList unitAssociationList = null;
|
|
815
|
if (item != null){
|
|
816
|
unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");
|
|
817
|
for(int k=0;k<unitAssociationList.getLength();k++){
|
|
818
|
if(unitAssociationList.item(k) instanceof Element){
|
|
819
|
Element unitAssociation = (Element)unitAssociationList.item(k);
|
|
820
|
UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, state.getReport(), state.getCdmRepository());
|
|
821
|
UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
|
|
822
|
|
|
823
|
state.setActualAccessPoint(associationWrapper.getAccesPoint());
|
|
824
|
if(associationWrapper!=null){
|
|
825
|
NodeList associatedUnits = associationWrapper.getAssociatedUnits();
|
|
826
|
if(associatedUnits!=null){
|
|
827
|
for(int m=0;m<associatedUnits.getLength();m++){
|
|
828
|
if(associatedUnits.item(m) instanceof Element){
|
|
829
|
state.reset();
|
|
830
|
state.setPrefix(associationWrapper.getPrefix());
|
|
831
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
|
|
832
|
logger.debug("derived unit: " + state.getDerivedUnitBase().toString() + " associated unit: " +state.getDataHolder().getKindOfUnit() + ", " + state.getDataHolder().accessionNumber + ", " + state.getDataHolder().getRecordBasis() + ", " + state.getDataHolder().getUnitID());
|
|
833
|
handleSingleUnit(state, associatedUnits.item(m), true);
|
|
834
|
|
|
835
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
836
|
FieldUnit associatedFieldUnit = null;
|
|
837
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid(), null);
|
|
838
|
//ignore field unit if associated unit has more than one
|
|
839
|
if(associatedFieldUnits.size()>1){
|
|
840
|
state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
841
|
}
|
|
842
|
else if(associatedFieldUnits.size()==1){
|
|
843
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
844
|
}
|
|
845
|
|
|
846
|
//attach current unit and associated unit depending on association type
|
|
847
|
|
|
848
|
//parent-child relation:
|
|
849
|
//copy derivation event and connect parent and sub derivative
|
|
850
|
// if(associationWrapper.getAssociationType().contains("individual") || associationWrapper.getAssociationType().contains("culture") || associationWrapper.getAssociationType().contains("sample") || associationWrapper.getAssociationType().contains("same in situ")){
|
|
851
|
if(currentDerivedFrom==null){
|
|
852
|
state.getReport().addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",SpecimenImportUtility.getUnitID(currentUnit, config)));
|
|
853
|
DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());
|
|
854
|
}
|
|
855
|
else{
|
|
856
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());
|
|
857
|
updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
858
|
updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
859
|
updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
860
|
updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
861
|
|
|
862
|
}
|
|
863
|
state.getReport().addDerivate(associatedUnit, currentUnit, config);
|
|
864
|
// }
|
|
865
|
//siblings relation
|
|
866
|
//connect current unit to field unit of associated unit
|
|
867
|
// else if(associationWrapper.getAssociationType().contains("population")|| associationWrapper.getAssociationType().contains("sample")){
|
|
868
|
// //no associated field unit -> using current one
|
|
869
|
// if(associatedFieldUnit==null){
|
|
870
|
// if(currentFieldUnit!=null){
|
|
871
|
// DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());
|
|
872
|
// }
|
|
873
|
// }
|
|
874
|
// else{
|
|
875
|
// if(currentDerivedFrom==null){
|
|
876
|
// state.getReport().addInfoMessage("No derivation event found for unit "+SpecimenImportUtility.getUnitID(currentUnit, config)+". Defaulting to ACCESIONING event.");
|
|
877
|
// DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());
|
|
878
|
// }
|
|
879
|
// if(currentDerivedFrom!=null && associatedFieldUnit==currentFieldUnit){
|
|
880
|
// DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());
|
|
881
|
// updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
882
|
// updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
883
|
// updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
884
|
// updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
885
|
// }
|
|
886
|
// }
|
|
887
|
// }
|
|
888
|
|
|
889
|
//delete current field unit if replaced
|
|
890
|
if(currentFieldUnit!=null && currentDerivedFrom!=null
|
|
891
|
&& currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit
|
|
892
|
&& currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units
|
|
893
|
&& currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted
|
|
894
|
){
|
|
895
|
currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
|
|
896
|
state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);
|
|
897
|
}
|
|
898
|
|
|
899
|
save(associatedUnit, state);
|
|
900
|
}
|
|
901
|
}
|
|
902
|
}
|
|
903
|
}
|
|
904
|
}
|
|
905
|
}
|
|
906
|
}
|
|
907
|
//TODO: pop state
|
|
908
|
state.reset();
|
|
909
|
state.setDerivedUnitBase(currentUnit);
|
|
910
|
state.setActualAccessPoint(currentAccessPoint);
|
|
911
|
state.setPrefix(currentPrefix);
|
|
912
|
}
|
|
913
|
|
|
914
|
|
|
915
|
|
|
916
|
|
|
917
|
/**
|
|
918
|
* @param derivedUnitFacade
|
|
919
|
* @param sour
|
|
920
|
* @return
|
|
921
|
*/
|
|
922
|
private boolean sourceNotLinkedToElement(DerivedUnitFacade derivedUnitFacade, OriginalSourceBase<?> source) {
|
|
923
|
Set<IdentifiableSource> linkedSources = derivedUnitFacade.getSources();
|
|
924
|
for (IdentifiableSource is:linkedSources){
|
|
925
|
if (is.getCitation()!=null && source.getCitation()!=null &&
|
|
926
|
is.getCitation().getTitleCache().equalsIgnoreCase(source.getCitation().getTitleCache())){
|
|
927
|
String isDetail = is.getCitationMicroReference();
|
|
928
|
if ((StringUtils.isBlank(isDetail) && StringUtils.isBlank(source.getCitationMicroReference()))
|
|
929
|
|| (isDetail != null && isDetail.equalsIgnoreCase(source.getCitationMicroReference())) ) {
|
|
930
|
return false;
|
|
931
|
}
|
|
932
|
}
|
|
933
|
}
|
|
934
|
return true;
|
|
935
|
}
|
|
936
|
|
|
937
|
|
|
938
|
|
|
939
|
// /**
|
|
940
|
// * @param reference
|
|
941
|
// * @param citationDetail
|
|
942
|
// * @return
|
|
943
|
// */
|
|
944
|
// private DescriptionElementSource getDescriptionSource(Reference reference, String citationDetail) {
|
|
945
|
//
|
|
946
|
// List<OriginalSourceBase> issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
947
|
//
|
|
948
|
// try {
|
|
949
|
// for (OriginalSourceBase<?> osb:issTmp2){
|
|
950
|
// if (osb.getCitation().equals(reference) && osb.getCitationMicroReference().equalsIgnoreCase(citationDetail)) {
|
|
951
|
// return (DescriptionElementSource) osb.clone();
|
|
952
|
// }
|
|
953
|
// }
|
|
954
|
// } catch (CloneNotSupportedException e) {
|
|
955
|
// // TODO Auto-generated catch block
|
|
956
|
// e.printStackTrace();
|
|
957
|
// }
|
|
958
|
//
|
|
959
|
// DescriptionElementSource sour = DescriptionElementSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
|
|
960
|
// return sour;
|
|
961
|
// }
|
|
962
|
|
|
963
|
|
|
964
|
|
|
965
|
|
|
966
|
/**
|
|
967
|
* setCollectionData : store the collection object into the
|
|
968
|
* derivedUnitFacade
|
|
969
|
*
|
|
970
|
* @param state
|
|
971
|
*/
|
|
972
|
protected void setCollectionData(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
|
|
973
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
974
|
SpecimenImportUtility.setUnitID(derivedUnitFacade.innerDerivedUnit(), state.getDataHolder().getUnitID(), config);
|
|
975
|
if(!config.isMapUnitIdToAccessionNumber()){
|
|
976
|
derivedUnitFacade.setAccessionNumber(NB(state.getDataHolder().accessionNumber));
|
|
977
|
}
|
|
978
|
// derivedUnitFacade.setCollectorsNumber(NB(state.getDataHolder().collectorsNumber));
|
|
979
|
|
|
980
|
/*
|
|
981
|
* INSTITUTION & COLLECTION
|
|
982
|
*/
|
|
983
|
// manage institution
|
|
984
|
Institution institution = this.getInstitution(NB(state.getDataHolder().institutionCode), state);
|
|
985
|
// manage collection
|
|
986
|
Collection collection = this.getCollection(institution, NB(state.getDataHolder().collectionCode), state);
|
|
987
|
// link specimen & collection
|
|
988
|
derivedUnitFacade.setCollection(collection);
|
|
989
|
}
|
|
990
|
|
|
991
|
/**
|
|
992
|
* getFacade : get the DerivedUnitFacade based on the recordBasis
|
|
993
|
* @param state
|
|
994
|
*
|
|
995
|
* @return DerivedUnitFacade
|
|
996
|
*/
|
|
997
|
@Override
|
|
998
|
protected DerivedUnitFacade getFacade(Abcd206ImportState state) {
|
|
999
|
if(logger.isDebugEnabled()) {
|
|
1000
|
logger.info("getFacade()");
|
|
1001
|
}
|
|
1002
|
SpecimenOrObservationType type = null;
|
|
1003
|
DefinedTerm kindOfUnit = null;
|
|
1004
|
|
|
1005
|
// create specimen
|
|
1006
|
if (NB((state.getDataHolder()).getRecordBasis()) != null) {
|
|
1007
|
if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
|
|
1008
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
1009
|
}
|
|
1010
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
|
|
1011
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
1012
|
}
|
|
1013
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
|
|
1014
|
type = SpecimenOrObservationType.Observation;
|
|
1015
|
}
|
|
1016
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
|
|
1017
|
type = SpecimenOrObservationType.Fossil;
|
|
1018
|
}else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("materialsample")>-1){
|
|
1019
|
type = SpecimenOrObservationType.OtherSpecimen;
|
|
1020
|
}
|
|
1021
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("sample")>-1){
|
|
1022
|
type = SpecimenOrObservationType.TissueSample;
|
|
1023
|
}
|
|
1024
|
|
|
1025
|
if (type == null) {
|
|
1026
|
logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
|
|
1027
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
1028
|
}
|
|
1029
|
} else {
|
|
1030
|
logger.info("The basis of record is null");
|
|
1031
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
1032
|
}
|
|
1033
|
|
|
1034
|
if (NB((state.getDataHolder()).getKindOfUnit()) != null) {
|
|
1035
|
kindOfUnit = getKindOfUnit(state, null, state.getDataHolder().getKindOfUnit().toLowerCase(), null, null, null);
|
|
1036
|
if (kindOfUnit == null){
|
|
1037
|
if (state.getDataHolder().getKindOfUnit().toLowerCase().indexOf("clone")>-1) {
|
|
1038
|
kindOfUnit = getKindOfUnit(state, null, "clone culture", "clone culture", "cc", null);
|
|
1039
|
}
|
|
1040
|
else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("live")) {
|
|
1041
|
kindOfUnit = getKindOfUnit(state, null, "live sample", "live sample", "ls", null);
|
|
1042
|
}
|
|
1043
|
else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("microscopic slide")) {
|
|
1044
|
kindOfUnit = getKindOfUnit(state, null, "microscopic slide", "microscopic slide", "ms", null);
|
|
1045
|
}
|
|
1046
|
|
|
1047
|
|
|
1048
|
if (kindOfUnit == null) {
|
|
1049
|
logger.info("The kind of unit does not seem to be known: " + state.getDataHolder().getKindOfUnit());
|
|
1050
|
|
|
1051
|
}
|
|
1052
|
}
|
|
1053
|
} else {
|
|
1054
|
logger.info("The kind of unit is null");
|
|
1055
|
|
|
1056
|
}
|
|
1057
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
1058
|
derivedUnitFacade.setFieldUnit(state.getFieldUnit(state.getDataHolder().getFieldNumber()));
|
|
1059
|
derivedUnitFacade.setKindOfUnit(kindOfUnit);
|
|
1060
|
return derivedUnitFacade;
|
|
1061
|
}
|
|
1062
|
|
|
1063
|
private void getCollectorsFromXML(Element root, Abcd206XMLFieldGetter abcdFieldGetter, Abcd206ImportState state) {
|
|
1064
|
NodeList group;
|
|
1065
|
|
|
1066
|
group = root.getChildNodes();
|
|
1067
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1068
|
if (group.item(i).getNodeName().equals(state.getPrefix() + "Identifications")) {
|
|
1069
|
group = group.item(i).getChildNodes();
|
|
1070
|
break;
|
|
1071
|
}
|
|
1072
|
}
|
|
1073
|
//state.getDataHolder().gatheringAgents = "";
|
|
1074
|
|
|
1075
|
abcdFieldGetter.getType(root);
|
|
1076
|
abcdFieldGetter.getGatheringPeople(root);
|
|
1077
|
}
|
|
1078
|
|
|
1079
|
|
|
1080
|
|
|
1081
|
// private void compareABCDtoCDM(URI urlFileName, List<String> knownElts, Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
1082
|
// try {
|
|
1083
|
// DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
|
|
1084
|
// DocumentBuilder constructeur = factory.newDocumentBuilder();
|
|
1085
|
// URL url = urlFileName.toURL();
|
|
1086
|
// Object o = url.getContent();
|
|
1087
|
// InputStream is = (InputStream) o;
|
|
1088
|
// Document document = constructeur.parse(is);
|
|
1089
|
// Element root = document.getDocumentElement();
|
|
1090
|
// abcdFieldGetter.traverse(root);
|
|
1091
|
// }
|
|
1092
|
// catch (ParserConfigurationException e){
|
|
1093
|
// e.printStackTrace();
|
|
1094
|
// }
|
|
1095
|
// catch (SAXException e) {
|
|
1096
|
// e.printStackTrace();
|
|
1097
|
// }
|
|
1098
|
// catch (IOException e) {
|
|
1099
|
// e.printStackTrace();
|
|
1100
|
// }
|
|
1101
|
// Set<String> elts = state.getDataHolder().allABCDelements.keySet();
|
|
1102
|
// Iterator<String> it = elts.iterator();
|
|
1103
|
// String elt;
|
|
1104
|
// while (it.hasNext()) {
|
|
1105
|
// elt = it.next();
|
|
1106
|
// if (knownElts.indexOf(elt) == -1) {
|
|
1107
|
// if(DEBUG) {
|
|
1108
|
// logger.info("Unmerged ABCD element: " + elt + " - "+ state.getDataHolder().allABCDelements.get(elt));
|
|
1109
|
// }
|
|
1110
|
// }
|
|
1111
|
// }
|
|
1112
|
// }
|
|
1113
|
|
|
1114
|
/**
|
|
1115
|
* Load the list of names from the ABCD file and save them
|
|
1116
|
* @param state : the current ABCD import state
|
|
1117
|
* @param unitsList : the unit list from the ABCD file
|
|
1118
|
* @param abcdFieldGetter : the ABCD parser
|
|
1119
|
*/
|
|
1120
|
private void prepareCollectors(Abcd206ImportState state, NodeList unitsList, Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
1121
|
|
|
1122
|
TeamOrPersonBase<?> teamOrPerson = null;
|
|
1123
|
Team team = null;
|
|
1124
|
//ImportHelper.setOriginalSource(teamOrPerson, state.getConfig().getSourceReference(), collector, "Collector");
|
|
1125
|
for (int i = 0; i < unitsList.getLength(); i++) {
|
|
1126
|
this.getCollectorsFromXML((Element) unitsList.item(i), abcdFieldGetter, state);
|
|
1127
|
if (!(state.getDataHolder().gatheringAgentsList.isEmpty())){
|
|
1128
|
if (state.getDataHolder().gatheringAgentsList.size() == 1){
|
|
1129
|
teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgentsList.get(0));
|
|
1130
|
}else{
|
|
1131
|
team = new Team();
|
|
1132
|
for(String collector: state.getDataHolder().gatheringAgentsList){
|
|
1133
|
teamOrPerson = parseAuthorString(collector);
|
|
1134
|
if (teamOrPerson instanceof Person){
|
|
1135
|
team.addTeamMember((Person)teamOrPerson);
|
|
1136
|
}else{
|
|
1137
|
for (Person person: ((Team)teamOrPerson).getTeamMembers()){
|
|
1138
|
team.addTeamMember(person);
|
|
1139
|
}
|
|
1140
|
}
|
|
1141
|
}
|
|
1142
|
}
|
|
1143
|
if (!state.getPersonStore().containsId(state.getDataHolder().gatheringAgentsList.toString())) {
|
|
1144
|
state.getPersonStore().put(state.getDataHolder().gatheringAgentsList.toString(), teamOrPerson);
|
|
1145
|
if (logger.isDebugEnabled()) { logger.debug("Stored author " + state.getDataHolder().gatheringAgentsList.toString());}
|
|
1146
|
logger.warn("Not imported author with duplicated aut_id " + state.getDataHolder().gatheringAgentsList.toString() );
|
|
1147
|
}
|
|
1148
|
}
|
|
1149
|
if (!StringUtils.isBlank(state.getDataHolder().gatheringAgentsText) && state.getDataHolder().gatheringAgentsList.isEmpty()){
|
|
1150
|
teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgentsText);
|
|
1151
|
}
|
|
1152
|
|
|
1153
|
}
|
|
1154
|
|
|
1155
|
|
|
1156
|
|
|
1157
|
|
|
1158
|
// List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
|
|
1159
|
// List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
|
|
1160
|
//
|
|
1161
|
//
|
|
1162
|
// //existing teams in DB
|
|
1163
|
// Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
|
|
1164
|
// List<UuidAndTitleCache<Team>> hiberTeam = new ArrayList<UuidAndTitleCache<Team>>();//getAgentService().getTeamUuidAndTitleCache();
|
|
1165
|
|
|
1166
|
// Set<UUID> uuids = new HashSet<UUID>();
|
|
1167
|
// for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
|
|
1168
|
// uuids.add(hibernateT.getUuid());
|
|
1169
|
// }
|
|
1170
|
// if (!uuids.isEmpty()){
|
|
1171
|
// List<AgentBase> existingTeams = getAgentService().find(uuids);
|
|
1172
|
// for (AgentBase<?> existingP:existingTeams){
|
|
1173
|
// titleCacheTeam.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Team.class));
|
|
1174
|
// }
|
|
1175
|
// }
|
|
1176
|
|
|
1177
|
|
|
1178
|
// Map<String,UUID> teamMap = new HashMap<String, UUID>();
|
|
1179
|
// for (UuidAndTitleCache<Team> uuidt:hiberTeam){
|
|
1180
|
// teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
|
|
1181
|
// }
|
|
1182
|
|
|
1183
|
//existing persons in DB
|
|
1184
|
// List<UuidAndTitleCache<Person>> hiberPersons = new ArrayList<UuidAndTitleCache<Person>>();//getAgentService().getPersonUuidAndTitleCache();
|
|
1185
|
// Map<String,Person> titleCachePerson = new HashMap<String, Person>();
|
|
1186
|
// uuids = new HashSet<UUID>();
|
|
1187
|
// for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
1188
|
// uuids.add(hibernateP.getUuid());
|
|
1189
|
// }
|
|
1190
|
//
|
|
1191
|
// if (!uuids.isEmpty()){
|
|
1192
|
// List<AgentBase> existingPersons = getAgentService().find(uuids);
|
|
1193
|
// for (AgentBase<?> existingP:existingPersons){
|
|
1194
|
// titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Person.class));
|
|
1195
|
// }
|
|
1196
|
// }
|
|
1197
|
//
|
|
1198
|
// Map<String,UUID> personMap = new HashMap<String, UUID>();
|
|
1199
|
// for (UuidAndTitleCache<Person> person:hiberPersons){
|
|
1200
|
// personMap.put(person.getTitleCache(), person.getUuid());
|
|
1201
|
// }
|
|
1202
|
//
|
|
1203
|
// java.util.Collection<Person> personToadd = new ArrayList<Person>();
|
|
1204
|
// java.util.Collection<Team> teamToAdd = new ArrayList<Team>();
|
|
1205
|
//
|
|
1206
|
// for (String collector:collectorsU){
|
|
1207
|
// Person p = Person.NewInstance();
|
|
1208
|
// p.setTitleCache(collector,true);
|
|
1209
|
// if (!personMap.containsKey(p.getTitleCache())){
|
|
1210
|
// personToadd.add(p);
|
|
1211
|
// }
|
|
1212
|
// }
|
|
1213
|
// for (String team:teamsU){
|
|
1214
|
// Team p = Team.NewInstance();
|
|
1215
|
// p.setTitleCache(team,true);
|
|
1216
|
// if (!teamMap.containsKey(p.getTitleCache())){
|
|
1217
|
// teamToAdd.add(p);
|
|
1218
|
// }
|
|
1219
|
// }
|
|
1220
|
//
|
|
1221
|
// if(!personToadd.isEmpty()){
|
|
1222
|
// for (Person agent: personToadd){
|
|
1223
|
// save(agent, state);
|
|
1224
|
// titleCachePerson.put(agent.getTitleCache(),CdmBase.deproxy(agent, Person.class) );
|
|
1225
|
// }
|
|
1226
|
// }
|
|
1227
|
//
|
|
1228
|
// Person ptmp ;
|
|
1229
|
// Map <String,Integer>teamdone = new HashMap<String, Integer>();
|
|
1230
|
// for (List<String> collteam: collectorinteams){
|
|
1231
|
// if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
|
|
1232
|
// Team team = new Team();
|
|
1233
|
// boolean em =true;
|
|
1234
|
// for (String collector:collteam){
|
|
1235
|
// ptmp = Person.NewInstance();
|
|
1236
|
// ptmp.setTitleCache(collector,true);
|
|
1237
|
// Person p2 = titleCachePerson.get(ptmp.getTitleCache());
|
|
1238
|
// team.addTeamMember(p2);
|
|
1239
|
// em=false;
|
|
1240
|
// }
|
|
1241
|
// if (!em) {
|
|
1242
|
// teamToAdd.add(team);
|
|
1243
|
// }
|
|
1244
|
// teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
|
|
1245
|
// }
|
|
1246
|
// }
|
|
1247
|
//
|
|
1248
|
// if(!teamToAdd.isEmpty()){
|
|
1249
|
// for (Team agent: teamToAdd){
|
|
1250
|
// save(agent, state);
|
|
1251
|
// titleCacheTeam.put(agent.getTitleCache(), CdmBase.deproxy( agent,Team.class) );
|
|
1252
|
// }
|
|
1253
|
// }
|
|
1254
|
|
|
1255
|
// ((Abcd206ImportConfigurator) state.getConfig()).setTeams(titleCacheTeam);
|
|
1256
|
// ((Abcd206ImportConfigurator) state.getConfig()).setPersons(titleCachePerson);
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
|
|
1260
|
@Override
|
|
1261
|
protected boolean doCheck(Abcd206ImportState state) {
|
|
1262
|
logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
|
|
1263
|
return true;
|
|
1264
|
}
|
|
1265
|
|
|
1266
|
@Override
|
|
1267
|
protected boolean isIgnore(Abcd206ImportState state) {
|
|
1268
|
return false;
|
|
1269
|
}
|
|
1270
|
|
|
1271
|
|
|
1272
|
@Override
|
|
1273
|
protected DefinedTerm getKindOfUnit(Abcd206ImportState state, UUID uuid, String label, String description, String labelAbbrev, TermVocabulary<DefinedTerm> voc){
|
|
1274
|
|
|
1275
|
DefinedTerm unit = null;
|
|
1276
|
|
|
1277
|
if (uuid == null){
|
|
1278
|
unit = this.kindOfUnitsMap.get(label.toLowerCase());
|
|
1279
|
}else{
|
|
1280
|
unit = state.getKindOfUnit(uuid);
|
|
1281
|
|
|
1282
|
}
|
|
1283
|
if (unit == null){
|
|
1284
|
unit = (DefinedTerm)getTermService().find(uuid);
|
|
1285
|
if (unit == null){
|
|
1286
|
if (uuid == null){
|
|
1287
|
uuid = UUID.randomUUID();
|
|
1288
|
}
|
|
1289
|
unit = DefinedTerm.NewKindOfUnitInstance(description, label, labelAbbrev);
|
|
1290
|
unit.setUuid(uuid);
|
|
1291
|
if (voc == null){
|
|
1292
|
boolean isOrdered = false;
|
|
1293
|
voc = getVocabulary(TermType.KindOfUnit, uuidUserDefinedKindOfUnitVocabulary, "User defined vocabulary for kind-of-units", "User Defined Measurement kind-of-units", null, null, isOrdered, unit);
|
|
1294
|
}
|
|
1295
|
voc.addTerm(unit);
|
|
1296
|
getTermService().save(unit);
|
|
1297
|
}
|
|
1298
|
state.putKindOfUnit(unit);
|
|
1299
|
kindOfUnitsMap.put(unit.getLabel().toLowerCase(), unit);
|
|
1300
|
}
|
|
1301
|
return unit;
|
|
1302
|
}
|
|
1303
|
|
|
1304
|
|
|
1305
|
}
|