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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.IOException;
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import java.io.InputStream;
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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.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.api.service.DeleteResult;
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import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
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import eu.etaxonomy.cdm.common.StreamUtils;
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import eu.etaxonomy.cdm.common.URI;
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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.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.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.media.RightsType;
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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.OriginalSourceBase;
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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.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author p.kelbert
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* @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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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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state.addImportReference(state.getRef());
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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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if (sourceUri != null) {
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state.getRef().setTitle(StringUtils.substringAfter(sourceUri.toString(), "dsa="));
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}
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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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state.addImportReference(state.getRef());
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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
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// classification was set in
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// config
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List<Classification> classificationList = getClassificationService().list(Classification.class, null,
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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(
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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
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// 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
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// 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,
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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(),
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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(
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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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commitTransaction(state.getTx());
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state.setTx(startTransaction());
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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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state.getDataHolder().setNomenclatureCode(state.getConfig().getNomenclaturalCode()!= null? state.getConfig().getNomenclaturalCode().getKey() : null);
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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
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+ "/" + 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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state.setLastFieldUnit(null);
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}
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commitTransaction(state.getTx());
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state.setTx(startTransaction());
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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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} 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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} finally {
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state.getReport().printReport(state.getConfig().getReportUri());
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}
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288
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if (state.getConfig().isDownloadSequenceData()) {
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for (URI uri : state.getSequenceDataStableIdentifier()) {
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// Files.createDirectories(file.getParent()); // optional, make
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// sure parent dir exists
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292
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try {
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StreamUtils.downloadFile(uri.toURL(), "temp");
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} catch (IOException e) {
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295
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// TODO Auto-generated catch block
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296
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e.printStackTrace();
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}
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298
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}
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300
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}
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301
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return;
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303
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}
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304
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305
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/**
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306
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*
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307
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*/
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308
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private void createKindOfUnitsMap(Abcd206ImportState state) {
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309
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310
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ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
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311
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if (cdmRepository == null) {
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cdmRepository = this;
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313
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}
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314
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315
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List<DefinedTerm> terms = cdmRepository.getTermService().listByTermType(TermType.KindOfUnit, null, 0, null,
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null);
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317
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kindOfUnitsMap = new HashMap<>();
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318
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for (DefinedTerm kindOfUnit : terms) {
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319
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if (kindOfUnit != null && kindOfUnit.getLabel() != null) {
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String kindOfUnitLabel = kindOfUnit.getLabel().toLowerCase();
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kindOfUnitsMap.put(kindOfUnitLabel, kindOfUnit);
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}
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323
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324
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}
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325
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}
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326
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327
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/**
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328
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* @param state
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329
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* @param item
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330
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*/
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331
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private void getSiblings(Abcd206ImportState state, Object item, DerivedUnitFacade facade) {
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332
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String unitId = facade.getCatalogNumber();
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333
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if (unitId == null) {
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unitId = facade.getAccessionNumber();
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335
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}
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336
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if (unitId == null){
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unitId = facade.getBarcode();
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338
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}
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339
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340
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UnitAssociationParser unitParser = new UnitAssociationParser(state.getPrefix(), state.getReport(),
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341
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state.getCdmRepository());
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342
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UnitAssociationWrapper unitAssociationWrapper = null;
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343
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for (URI accessPoint : state.getAllAccesPoint()) {
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344
|
unitAssociationWrapper = unitParser.parseSiblings(unitId, accessPoint);
|
|
345
|
if (unitAssociationWrapper != null && unitAssociationWrapper.getAssociatedUnits() != null) {
|
|
346
|
break;
|
|
347
|
}
|
|
348
|
}
|
|
349
|
|
|
350
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
351
|
// DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
352
|
FieldUnit currentFieldUnit = facade.getFieldUnit(false);
|
|
353
|
if (unitAssociationWrapper != null) {
|
|
354
|
NodeList associatedUnits = unitAssociationWrapper.getAssociatedUnits();
|
|
355
|
if (associatedUnits != null) {
|
|
356
|
for (int m = 0; m < associatedUnits.getLength(); m++) {
|
|
357
|
if (associatedUnits.item(m) instanceof Element) {
|
|
358
|
state.reset();
|
|
359
|
String associationType = AbcdParseUtility
|
|
360
|
.parseFirstTextContent(((Element) associatedUnits.item(m))
|
|
361
|
.getElementsByTagName(state.getPrefix() + "AssociationType"));
|
|
362
|
|
|
363
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m),
|
|
364
|
new Abcd206XMLFieldGetter(state.getDataHolder(), unitAssociationWrapper.getPrefix()),
|
|
365
|
state);
|
|
366
|
// logger.debug("derived unit: " +
|
|
367
|
// state.getDerivedUnitBase().toString() + " associated
|
|
368
|
// unit: " +state.getDataHolder().getKindOfUnit() + ", "
|
|
369
|
// + state.getDataHolder().accessionNumber + ", " +
|
|
370
|
// state.getDataHolder().getRecordBasis() + ", " +
|
|
371
|
// state.getDataHolder().getUnitID());
|
|
372
|
|
|
373
|
handleSingleUnit(state, associatedUnits.item(m), false);
|
|
374
|
|
|
375
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
376
|
FieldUnit associatedFieldUnit = null;
|
|
377
|
commitTransaction(state.getTx());
|
|
378
|
state.setTx(startTransaction());
|
|
379
|
java.util.Collection<FieldUnit> associatedFieldUnits = null;
|
|
380
|
try {
|
|
381
|
associatedFieldUnits = state.getCdmRepository().getOccurrenceService()
|
|
382
|
.findFieldUnits(associatedUnit.getUuid(), null);
|
|
383
|
} catch (NullPointerException e) {
|
|
384
|
logger.error("Search for associated field unit creates a NPE" + e.getMessage());
|
|
385
|
}
|
|
386
|
// ignore field unit if associated unit has more than
|
|
387
|
// one
|
|
388
|
if (associatedFieldUnits != null && associatedFieldUnits.size() > 1) {
|
|
389
|
state.getReport()
|
|
390
|
.addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
391
|
} else if (associatedFieldUnits != null && associatedFieldUnits.size() == 1) {
|
|
392
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
393
|
}
|
|
394
|
// parent-child relation:
|
|
395
|
if (associationType != null && (associationType.contains("individual") || associationType.contains("culture")
|
|
396
|
|| associationType.contains("sample") || associationType.contains("isolated"))) {
|
|
397
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(currentUnit,
|
|
398
|
associatedUnit, DerivationEventType.ACCESSIONING());
|
|
399
|
|
|
400
|
updatedDerivationEvent.setDescription(associationType);
|
|
401
|
if (associatedFieldUnit != null && associatedFieldUnit != currentFieldUnit && currentFieldUnit != null) {
|
|
402
|
// associatedFieldUnit.removeDerivationEvent(updatedDerivationEvent);
|
|
403
|
// save(associatedFieldUnit, state);
|
|
404
|
// if
|
|
405
|
// (associatedFieldUnit.getDerivationEvents().isEmpty()){
|
|
406
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
407
|
config.setDeleteChildren(false);
|
|
408
|
DeleteResult result = state.getCdmRepository().getOccurrenceService()
|
|
409
|
.delete(associatedFieldUnit, config);
|
|
410
|
if (!result.isOk()) {
|
|
411
|
logger.debug("Deletion of field unit " + associatedFieldUnit.getFieldNumber()
|
|
412
|
+ " not successfull");
|
|
413
|
}
|
|
414
|
state.setFieldUnit(currentFieldUnit);
|
|
415
|
|
|
416
|
// }
|
|
417
|
|
|
418
|
}
|
|
419
|
state.getReport().addDerivate(associatedUnit, currentUnit, state.getConfig());
|
|
420
|
}
|
|
421
|
save(associatedUnit, state);
|
|
422
|
|
|
423
|
}
|
|
424
|
}
|
|
425
|
}
|
|
426
|
}
|
|
427
|
state.reset();
|
|
428
|
state.setDerivedUnitBase(currentUnit);
|
|
429
|
|
|
430
|
}
|
|
431
|
|
|
432
|
/**
|
|
433
|
* Handle a single unit
|
|
434
|
*
|
|
435
|
* @param state
|
|
436
|
* @param item
|
|
437
|
*/
|
|
438
|
@Override
|
|
439
|
public void handleSingleUnit(Abcd206ImportState state, Object itemObject) {
|
|
440
|
handleSingleUnit(state, itemObject, true);
|
|
441
|
}
|
|
442
|
|
|
443
|
@SuppressWarnings("rawtypes")
|
|
444
|
public void handleSingleUnit(Abcd206ImportState state, Object itemObject, boolean handleAssociatedUnits) {
|
|
445
|
Element item = (Element) itemObject;
|
|
446
|
|
|
447
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
448
|
if (logger.isDebugEnabled()) {
|
|
449
|
logger.info("handleSingleUnit " + state.getRef());
|
|
450
|
}
|
|
451
|
try {
|
|
452
|
ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
|
|
453
|
if (cdmAppController == null) {
|
|
454
|
cdmAppController = this;
|
|
455
|
}
|
|
456
|
// check if unit already exists
|
|
457
|
DerivedUnitFacade derivedUnitFacade = null;
|
|
458
|
if (state.getConfig().isIgnoreImportOfExistingSpecimen() && state.getDataHolder().getUnitID() != null) {
|
|
459
|
|
|
460
|
SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(state.getDataHolder().getUnitID(),
|
|
461
|
state);
|
|
462
|
if (existingSpecimen != null && existingSpecimen.isInstanceOf(DerivedUnit.class)) {
|
|
463
|
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);
|
|
464
|
state.setDerivedUnitBase(derivedUnit);
|
|
465
|
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
|
|
466
|
if (handleAssociatedUnits) {
|
|
467
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
468
|
}
|
|
469
|
if (state.getConfig().getDnaSoure() != null) {
|
|
470
|
importAssociatedDna(state, item, derivedUnitFacade);
|
|
471
|
}
|
|
472
|
|
|
473
|
state.getReport().addAlreadyExistingSpecimen(SpecimenImportUtility.getUnitID(derivedUnit, config),
|
|
474
|
derivedUnit);
|
|
475
|
|
|
476
|
return;
|
|
477
|
}
|
|
478
|
} else {
|
|
479
|
System.err.println("dataholder does not contain unit id");
|
|
480
|
}
|
|
481
|
|
|
482
|
|
|
483
|
// import DNA unit
|
|
484
|
if (state.getDataHolder().getKindOfUnit() != null
|
|
485
|
&& state.getDataHolder().getKindOfUnit().equalsIgnoreCase("dna")) {
|
|
486
|
AbcdDnaParser dnaParser = new AbcdDnaParser(state.getPrefix(), state.getReport(),
|
|
487
|
state.getCdmRepository());
|
|
488
|
DnaSample dnaSample = dnaParser.parse(item, state);
|
|
489
|
//dnaSample.addSource(OriginalSourceType.Import, dnaSample.getAccessionNumber(), "", state.getImportReference(state.getActualAccessPoint()), "");
|
|
490
|
save(dnaSample, state);
|
|
491
|
// set dna as derived unit to avoid creating an extra specimen
|
|
492
|
// for this dna sample (instead just the field unit will be
|
|
493
|
// created)
|
|
494
|
state.setDerivedUnitBase(dnaSample);
|
|
495
|
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
|
|
496
|
} else {
|
|
497
|
// create facade
|
|
498
|
derivedUnitFacade = getFacade(state);
|
|
499
|
state.setDerivedUnitBase(derivedUnitFacade.innerDerivedUnit());
|
|
500
|
|
|
501
|
}
|
|
502
|
|
|
503
|
/**
|
|
504
|
* GATHERING EVENT
|
|
505
|
*/
|
|
506
|
|
|
507
|
// look for existing fieldUnit
|
|
508
|
FieldUnit fieldUnit = null;
|
|
509
|
if (StringUtils.isNotBlank(state.getDataHolder().getFieldNumber())){
|
|
510
|
fieldUnit = state.getFieldUnit(state.getDataHolder().getFieldNumber());
|
|
511
|
if (fieldUnit != null){
|
|
512
|
state.setLastFieldUnit(fieldUnit);
|
|
513
|
}
|
|
514
|
}else{
|
|
515
|
fieldUnit = state.getLastFieldUnit();
|
|
516
|
|
|
517
|
}
|
|
518
|
if (fieldUnit == null){
|
|
519
|
fieldUnit = FieldUnit.NewInstance();
|
|
520
|
fieldUnit.setFieldNumber(state.getDataHolder().getFieldNumber());
|
|
521
|
state.setLastFieldUnit(fieldUnit);
|
|
522
|
}
|
|
523
|
|
|
524
|
// gathering event
|
|
525
|
UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(cdmAppController.getTermService(),
|
|
526
|
state.getDataHolder().locality, state.getDataHolder().languageIso, state.getDataHolder().longitude,
|
|
527
|
state.getDataHolder().latitude, state.getDataHolder().getGatheringCoordinateErrorMethod(),
|
|
528
|
state.getDataHolder().getGatheringElevationText(), state.getDataHolder().getGatheringElevationMin(),
|
|
529
|
state.getDataHolder().getGatheringElevationMax(), state.getDataHolder().getGatheringElevationUnit(),
|
|
530
|
state.getDataHolder().getGatheringDateText(), state.getDataHolder().getGatheringNotes(),
|
|
531
|
state.getDataHolder().getGatheringMethod(),
|
|
532
|
state.getTransformer().getReferenceSystemByKey(state.getDataHolder().getGatheringSpatialDatum()),
|
|
533
|
state.getConfig());
|
|
534
|
|
|
535
|
unitsGatheringEvent.setGatheringDepth(state.getDataHolder().getGatheringDepthText(),
|
|
536
|
state.getDataHolder().getGatheringDepthMin(), state.getDataHolder().getGatheringDepthMax(),
|
|
537
|
state.getDataHolder().getGatheringDepthUnit());
|
|
538
|
// unitsGatheringEvent.setHeight(heightText, heightMin, heightMax,
|
|
539
|
// heightUnit);
|
|
540
|
if (state.getDataHolder().gatheringAgentsList.isEmpty()) {
|
|
541
|
TeamOrPersonBase team = state.getPersonStore().get(state.getDataHolder().gatheringAgentsText);
|
|
542
|
if (team == null){
|
|
543
|
team = parseAuthorString(state.getDataHolder().gatheringAgentsText);
|
|
544
|
if (team != null){
|
|
545
|
state.getPersonStore().put(team.getTitleCache(), team);
|
|
546
|
}
|
|
547
|
}
|
|
548
|
if (team != null){
|
|
549
|
unitsGatheringEvent.setCollector(team,
|
|
550
|
config);
|
|
551
|
}
|
|
552
|
|
|
553
|
|
|
554
|
} else {
|
|
555
|
TeamOrPersonBase team = state.getPersonStore().get(state.getDataHolder().gatheringAgentsList.toString());
|
|
556
|
if (team == null){
|
|
557
|
team = parseAuthorString(state.getDataHolder().gatheringAgentsList.toString());
|
|
558
|
if (team != null){
|
|
559
|
state.getPersonStore().put(team.getTitleCache(), team);
|
|
560
|
}
|
|
561
|
|
|
562
|
}
|
|
563
|
if (team != null){
|
|
564
|
unitsGatheringEvent.setCollector(team,
|
|
565
|
config);
|
|
566
|
}
|
|
567
|
}
|
|
568
|
// count
|
|
569
|
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
|
|
570
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),
|
|
571
|
// getTermService());
|
|
572
|
unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country,
|
|
573
|
(state.getConfig()), cdmAppController.getTermService(),
|
|
574
|
cdmAppController.getVocabularyService());
|
|
575
|
|
|
576
|
DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();
|
|
577
|
|
|
578
|
// other areas
|
|
579
|
unitsGatheringArea = new UnitsGatheringArea();
|
|
580
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());
|
|
581
|
|
|
582
|
unitsGatheringArea.setAreas(state.getDataHolder().getNamedAreaList(), (state.getConfig()),
|
|
583
|
cdmAppController.getTermService(), cdmAppController.getVocabularyService());
|
|
584
|
|
|
585
|
ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
|
|
586
|
for (DefinedTermBase namedArea : nas) {
|
|
587
|
unitsGatheringEvent.addArea(namedArea);
|
|
588
|
}
|
|
589
|
|
|
590
|
// copy gathering event to facade
|
|
591
|
GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
|
|
592
|
if (fieldUnit != null) {
|
|
593
|
derivedUnitFacade.setFieldUnit(fieldUnit);
|
|
594
|
if (derivedUnitFacade.getGatheringPeriod() == null && gatheringEvent.getTimeperiod() != null){
|
|
595
|
derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
|
|
596
|
}
|
|
597
|
if (derivedUnitFacade.getLocality() == null && gatheringEvent.getLocality() != null){
|
|
598
|
derivedUnitFacade.setLocality(gatheringEvent.getLocality());
|
|
599
|
}
|
|
600
|
if (derivedUnitFacade.getExactLocation() == null && gatheringEvent.getExactLocation() != null){
|
|
601
|
derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
|
|
602
|
}
|
|
603
|
|
|
604
|
if (derivedUnitFacade.getCollector() == null && gatheringEvent.getCollector() != null){
|
|
605
|
derivedUnitFacade.setCollector(gatheringEvent.getCollector());
|
|
606
|
}
|
|
607
|
if (derivedUnitFacade.getCountry() == null && areaCountry != null){
|
|
608
|
derivedUnitFacade.setCountry((NamedArea) areaCountry);
|
|
609
|
}
|
|
610
|
if (StringUtils.isBlank(derivedUnitFacade.getAbsoluteElevationText()) && StringUtils.isNotBlank(gatheringEvent.getAbsoluteElevationText())){
|
|
611
|
derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());
|
|
612
|
}
|
|
613
|
if (derivedUnitFacade.getAbsoluteElevation() == null && gatheringEvent.getAbsoluteElevation() != null){
|
|
614
|
derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());
|
|
615
|
}
|
|
616
|
if (derivedUnitFacade.getAbsoluteElevationMaximum() == null && gatheringEvent.getAbsoluteElevationMax() != null){
|
|
617
|
derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());
|
|
618
|
}
|
|
619
|
if (StringUtils.isBlank(derivedUnitFacade.getDistanceToGroundText()) && StringUtils.isNotBlank(gatheringEvent.getDistanceToGroundText())){
|
|
620
|
derivedUnitFacade.setDistanceToGroundText(gatheringEvent.getDistanceToGroundText());
|
|
621
|
}
|
|
622
|
if (derivedUnitFacade.getDistanceToGroundMax() == null && gatheringEvent.getDistanceToGroundMax() != null){
|
|
623
|
derivedUnitFacade.setDistanceToGroundMax(gatheringEvent.getDistanceToGroundMax());
|
|
624
|
}
|
|
625
|
if (derivedUnitFacade.getDistanceToGround() == null && gatheringEvent.getDistanceToGround() != null){
|
|
626
|
derivedUnitFacade.setDistanceToGround(gatheringEvent.getDistanceToGround());
|
|
627
|
}
|
|
628
|
if (StringUtils.isBlank(derivedUnitFacade.getDistanceToWaterSurfaceText()) && StringUtils.isNotBlank(gatheringEvent.getDistanceToWaterSurfaceText())){
|
|
629
|
derivedUnitFacade.setDistanceToWaterSurfaceText(gatheringEvent.getDistanceToWaterSurfaceText());
|
|
630
|
}
|
|
631
|
if (derivedUnitFacade.getDistanceToWaterSurfaceMax() == null && gatheringEvent.getDistanceToWaterSurfaceMax() != null){
|
|
632
|
derivedUnitFacade.setDistanceToWaterSurfaceMax(gatheringEvent.getDistanceToWaterSurfaceMax());
|
|
633
|
}
|
|
634
|
if (derivedUnitFacade.getDistanceToWaterSurface() == null && gatheringEvent.getDistanceToWaterSurface() != null){
|
|
635
|
derivedUnitFacade.setDistanceToWaterSurface(gatheringEvent.getDistanceToWaterSurface());
|
|
636
|
}
|
|
637
|
if (derivedUnitFacade.getGatheringPeriod() == null && gatheringEvent.getTimeperiod() != null){
|
|
638
|
derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
|
|
639
|
}
|
|
640
|
if (derivedUnitFacade.getCollectingMethod() == null && gatheringEvent.getCollectingMethod() != null){
|
|
641
|
derivedUnitFacade.setCollectingMethod(gatheringEvent.getCollectingMethod());
|
|
642
|
}
|
|
643
|
for (DefinedTermBase<?> area : unitsGatheringArea.getAreas()) {
|
|
644
|
derivedUnitFacade.addCollectingArea((NamedArea) area);
|
|
645
|
}
|
|
646
|
// add unitNotes
|
|
647
|
if (state.getDataHolder().getUnitNotes() != null) {
|
|
648
|
derivedUnitFacade
|
|
649
|
.addAnnotation(Annotation.NewDefaultLanguageInstance(NB(state.getDataHolder().getUnitNotes())));
|
|
650
|
}
|
|
651
|
if (gatheringEvent.getAnnotations() != null) {
|
|
652
|
for (Annotation annotation : gatheringEvent.getAnnotations()) {
|
|
653
|
derivedUnitFacade.getGatheringEvent(true).addAnnotation(annotation);
|
|
654
|
}
|
|
655
|
}
|
|
656
|
|
|
657
|
}else{
|
|
658
|
//TODO??
|
|
659
|
}
|
|
660
|
|
|
661
|
|
|
662
|
|
|
663
|
|
|
664
|
// derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
|
|
665
|
// TODO exsiccatum
|
|
666
|
|
|
667
|
// add fieldNumber
|
|
668
|
String fieldNumber = null;
|
|
669
|
if (derivedUnitFacade.getFieldUnit(false) != null) {
|
|
670
|
fieldNumber = derivedUnitFacade.getFieldUnit(false).getFieldNumber();
|
|
671
|
if (fieldNumber == null){
|
|
672
|
derivedUnitFacade.setFieldNumber(NB(state.getDataHolder().getFieldNumber()));
|
|
673
|
}
|
|
674
|
}
|
|
675
|
|
|
676
|
save(unitsGatheringEvent.getLocality(), state);
|
|
677
|
|
|
678
|
|
|
679
|
|
|
680
|
|
|
681
|
// //add Multimedia URLs
|
|
682
|
if (state.getDataHolder().getMultimediaObjects().size() != -1) {
|
|
683
|
for (String multimediaObject : state.getDataHolder().getMultimediaObjects().keySet()) {
|
|
684
|
Media media;
|
|
685
|
try {
|
|
686
|
media = extractMedia(state, multimediaObject);
|
|
687
|
if (media == null) {
|
|
688
|
continue;
|
|
689
|
}
|
|
690
|
derivedUnitFacade.addDerivedUnitMedia(media);
|
|
691
|
if (state.getConfig().isAddMediaAsMediaSpecimen()) {
|
|
692
|
// add media also as specimen scan
|
|
693
|
MediaSpecimen mediaSpecimen = MediaSpecimen
|
|
694
|
.NewInstance(SpecimenOrObservationType.StillImage);
|
|
695
|
mediaSpecimen.setMediaSpecimen(media);
|
|
696
|
// do it only once!!
|
|
697
|
DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);
|
|
698
|
if (specimenScanTerm instanceof DefinedTerm) {
|
|
699
|
mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
|
|
700
|
}
|
|
701
|
DerivationEvent derivationEvent = DerivationEvent
|
|
702
|
.NewInstance(DerivationEventType.PREPARATION());
|
|
703
|
derivationEvent.addDerivative(mediaSpecimen);
|
|
704
|
derivedUnitFacade.innerDerivedUnit().addDerivationEvent(derivationEvent);
|
|
705
|
}
|
|
706
|
|
|
707
|
} catch (MalformedURLException e) {
|
|
708
|
// TODO Auto-generated catch block
|
|
709
|
e.printStackTrace();
|
|
710
|
}
|
|
711
|
|
|
712
|
}
|
|
713
|
}
|
|
714
|
// multimedia for fieldUnit
|
|
715
|
if (state.getDataHolder().getGatheringMultimediaObjects().size() != -1) {
|
|
716
|
for (String multimediaObject : state.getDataHolder().getGatheringMultimediaObjects().keySet()) {
|
|
717
|
Media media;
|
|
718
|
try {
|
|
719
|
media = extractMedia(state, multimediaObject);
|
|
720
|
if (media == null) {
|
|
721
|
continue;
|
|
722
|
}
|
|
723
|
derivedUnitFacade.addFieldObjectMedia(media);
|
|
724
|
|
|
725
|
} catch (MalformedURLException e) {
|
|
726
|
// TODO Auto-generated catch block
|
|
727
|
e.printStackTrace();
|
|
728
|
}
|
|
729
|
|
|
730
|
}
|
|
731
|
}
|
|
732
|
|
|
733
|
|
|
734
|
if (derivedUnitFacade.getFieldUnit(false) != null) {
|
|
735
|
state.setFieldUnit(derivedUnitFacade.getFieldUnit(false));
|
|
736
|
}
|
|
737
|
|
|
738
|
// handle collection data
|
|
739
|
setCollectionData(state, derivedUnitFacade);
|
|
740
|
|
|
741
|
// Reference stuff
|
|
742
|
SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
|
|
743
|
Map<String, OriginalSourceBase> sourceMap = new HashMap<>();
|
|
744
|
|
|
745
|
state.getDataHolder().setDocSources(new ArrayList<>());
|
|
746
|
|
|
747
|
|
|
748
|
|
|
749
|
IdentifiableSource sour = getIdentifiableSource(state.getImportReference(state.getActualAccessPoint()), null);
|
|
750
|
String idInSource = derivedUnitFacade.getAccessionNumber() != null ? derivedUnitFacade.getAccessionNumber()
|
|
751
|
: derivedUnitFacade.getCatalogNumber() != null ? derivedUnitFacade.getCatalogNumber() : derivedUnitFacade.getBarcode();
|
|
752
|
//sour.getCitation().setUri(state.getActualAccessPoint());
|
|
753
|
sour.setIdInSource(idInSource);
|
|
754
|
try {
|
|
755
|
if (sour.getCitation() != null) {
|
|
756
|
if (StringUtils.isNotBlank(sour.getCitationMicroReference())) {
|
|
757
|
state.getDataHolder().getDocSources()
|
|
758
|
.add(sour.getCitation().getTitleCache() + "---" + sour.getCitationMicroReference());
|
|
759
|
} else {
|
|
760
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache());
|
|
761
|
}
|
|
762
|
}
|
|
763
|
} catch (Exception e) {
|
|
764
|
logger.warn("oups");
|
|
765
|
}
|
|
766
|
|
|
767
|
derivedUnitFacade.addSource(sour);
|
|
768
|
|
|
769
|
|
|
770
|
save(state.getDerivedUnitBase(), state);
|
|
771
|
|
|
772
|
if (logger.isDebugEnabled()) {
|
|
773
|
logger.info("saved ABCD specimen ...");
|
|
774
|
}
|
|
775
|
|
|
776
|
// handle identifications
|
|
777
|
handleIdentifications(state, derivedUnitFacade);
|
|
778
|
|
|
779
|
// associatedUnits
|
|
780
|
if (handleAssociatedUnits) {
|
|
781
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
782
|
}
|
|
783
|
if (state.getConfig().getDnaSoure() != null ) {
|
|
784
|
boolean uriCorrect = true;
|
|
785
|
try{
|
|
786
|
state.getConfig().getDnaSoure().toString();
|
|
787
|
}catch(Exception e){
|
|
788
|
uriCorrect = false;
|
|
789
|
}
|
|
790
|
if (uriCorrect){
|
|
791
|
try{
|
|
792
|
importAssociatedDna(state, item, derivedUnitFacade);
|
|
793
|
}catch(Exception e){
|
|
794
|
String message = "Error when importing Dna! " + itemObject.toString();
|
|
795
|
state.getReport().addException(message, e);
|
|
796
|
state.setUnsuccessfull();
|
|
797
|
}
|
|
798
|
}
|
|
799
|
|
|
800
|
}
|
|
801
|
// siblings/ other children
|
|
802
|
if (derivedUnitFacade.getType() != null
|
|
803
|
&& (derivedUnitFacade.getType().equals(SpecimenOrObservationType.LivingSpecimen)
|
|
804
|
|| derivedUnitFacade.getType().equals(SpecimenOrObservationType.TissueSample)
|
|
805
|
|| derivedUnitFacade.getType().equals(SpecimenOrObservationType.OtherSpecimen)
|
|
806
|
|| derivedUnitFacade.getType().equals(SpecimenOrObservationType.MaterialSample))
|
|
807
|
&& state.getConfig().isGetSiblings()) {
|
|
808
|
getSiblings(state, item, derivedUnitFacade);
|
|
809
|
}
|
|
810
|
|
|
811
|
} catch (Exception e) {
|
|
812
|
String message = "Error when reading record! " + itemObject.toString();
|
|
813
|
state.getReport().addException(message, e);
|
|
814
|
state.setUnsuccessfull();
|
|
815
|
}
|
|
816
|
|
|
817
|
return;
|
|
818
|
}
|
|
819
|
|
|
820
|
/**
|
|
821
|
* @param state
|
|
822
|
* @param multimediaObject
|
|
823
|
* @return
|
|
824
|
* @throws MalformedURLException
|
|
825
|
*/
|
|
826
|
private Media extractMedia(Abcd206ImportState state, String multimediaObject) throws MalformedURLException {
|
|
827
|
Media media;
|
|
828
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
829
|
|
|
830
|
Map<String, String> attributes = state.getDataHolder().getMultimediaObjects().get(multimediaObject);
|
|
831
|
if (attributes == null) {
|
|
832
|
attributes = state.getDataHolder().getGatheringMultimediaObjects().get(multimediaObject);
|
|
833
|
if (attributes == null) {
|
|
834
|
logger.error(multimediaObject + " does not exist in dataHolder");
|
|
835
|
state.getResult().addError(multimediaObject + " does not exist in dataHolder");
|
|
836
|
return null;
|
|
837
|
}
|
|
838
|
}
|
|
839
|
if (attributes.containsKey("Context")) {
|
|
840
|
LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
|
|
841
|
media.putDescription(description);
|
|
842
|
}
|
|
843
|
if (attributes.containsKey("Comment")) {
|
|
844
|
LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
|
|
845
|
media.putDescription(description);
|
|
846
|
}
|
|
847
|
if (attributes.containsKey("Creators")) {
|
|
848
|
String creators = attributes.get("Creators");
|
|
849
|
Person artist;
|
|
850
|
Team artistTeam;
|
|
851
|
String[] artists;
|
|
852
|
if (creators != null) {
|
|
853
|
if (creators.contains("&")) {
|
|
854
|
artists = creators.split("&");
|
|
855
|
artistTeam = new Team();
|
|
856
|
for (String creator : artists) {
|
|
857
|
artist = Person.NewTitledInstance(creator);
|
|
858
|
artistTeam.addTeamMember(artist);
|
|
859
|
}
|
|
860
|
media.setArtist(artistTeam);
|
|
861
|
} else {
|
|
862
|
|
|
863
|
artist = Person.NewTitledInstance(creators);
|
|
864
|
media.setArtist(artist);
|
|
865
|
}
|
|
866
|
}
|
|
867
|
|
|
868
|
}
|
|
869
|
if (attributes.containsKey("CreateDate")) {
|
|
870
|
String createDate = attributes.get("CreateDate");
|
|
871
|
|
|
872
|
if (createDate != null) {
|
|
873
|
|
|
874
|
media.setMediaCreated(TimePeriodParser.parseString(createDate));
|
|
875
|
}
|
|
876
|
|
|
877
|
}
|
|
878
|
|
|
879
|
if (attributes.containsKey("License")) {
|
|
880
|
String licence = attributes.get("License");
|
|
881
|
|
|
882
|
if (licence != null) {
|
|
883
|
Rights right = Rights.NewInstance(licence, Language.ENGLISH(), RightsType.LICENSE());
|
|
884
|
media.addRights(right);
|
|
885
|
}
|
|
886
|
|
|
887
|
}
|
|
888
|
return media;
|
|
889
|
}
|
|
890
|
|
|
891
|
@Override
|
|
892
|
protected void importAssociatedUnits(Abcd206ImportState state, Object itemObject,
|
|
893
|
DerivedUnitFacade derivedUnitFacade) {
|
|
894
|
SpecimenDeleteConfigurator deleteConfig = new SpecimenDeleteConfigurator();
|
|
895
|
deleteConfig.setDeleteChildren(false);
|
|
896
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
897
|
// import associated units
|
|
898
|
FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();
|
|
899
|
// TODO: push state (think of implementing stack architecture for state
|
|
900
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
901
|
DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
902
|
URI currentAccessPoint = state.getActualAccessPoint();
|
|
903
|
String currentPrefix = state.getPrefix();
|
|
904
|
Element item = null;
|
|
905
|
if (itemObject instanceof Element) {
|
|
906
|
item = (Element) itemObject;
|
|
907
|
}
|
|
908
|
NodeList unitAssociationList = null;
|
|
909
|
if (item != null) {
|
|
910
|
unitAssociationList = item.getElementsByTagName(currentPrefix + "UnitAssociation");
|
|
911
|
for (int k = 0; k < unitAssociationList.getLength(); k++) {
|
|
912
|
if (unitAssociationList.item(k) instanceof Element) {
|
|
913
|
Element unitAssociation = (Element) unitAssociationList.item(k);
|
|
914
|
UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix,
|
|
915
|
state.getReport(), state.getCdmRepository());
|
|
916
|
UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
|
|
917
|
if (associationWrapper != null) {
|
|
918
|
state.setActualAccessPoint(associationWrapper.getAccesPoint());
|
|
919
|
NodeList associatedUnits = associationWrapper.getAssociatedUnits();
|
|
920
|
if (associatedUnits != null) {
|
|
921
|
for (int m = 0; m < associatedUnits.getLength(); m++) {
|
|
922
|
if (associatedUnits.item(m) instanceof Element) {
|
|
923
|
state.reset();
|
|
924
|
state.setPrefix(associationWrapper.getPrefix());
|
|
925
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m),
|
|
926
|
new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
|
|
927
|
// logger.debug("derived unit: " +
|
|
928
|
// state.getDerivedUnitBase().toString()
|
|
929
|
// + " associated unit: " +
|
|
930
|
// state.getDataHolder().getKindOfUnit() +
|
|
931
|
// ", "
|
|
932
|
// + state.getDataHolder().accessionNumber +
|
|
933
|
// ", "
|
|
934
|
// + state.getDataHolder().getRecordBasis()
|
|
935
|
// + ", "
|
|
936
|
// + state.getDataHolder().getUnitID());
|
|
937
|
handleSingleUnit(state, associatedUnits.item(m), true);
|
|
938
|
|
|
939
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
940
|
FieldUnit associatedFieldUnit = null;
|
|
941
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository()
|
|
942
|
.getOccurrenceService().findFieldUnits(associatedUnit.getUuid(), null);
|
|
943
|
// ignore field unit if associated unit has
|
|
944
|
// more than one
|
|
945
|
if (associatedFieldUnits != null && associatedFieldUnits.size() > 1) {
|
|
946
|
state.getReport().addInfoMessage(
|
|
947
|
String.format("%s has more than one field unit.", associatedUnit));
|
|
948
|
} else if (associatedFieldUnits != null && associatedFieldUnits.size() == 1) {
|
|
949
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
950
|
}
|
|
951
|
|
|
952
|
// attach current unit and associated unit
|
|
953
|
// depending on association type
|
|
954
|
|
|
955
|
// parent-child relation:
|
|
956
|
// copy derivation event and connect parent
|
|
957
|
// and sub derivative
|
|
958
|
// if(associationWrapper.getAssociationType().contains("individual")
|
|
959
|
// ||
|
|
960
|
// associationWrapper.getAssociationType().contains("culture")
|
|
961
|
// ||
|
|
962
|
// associationWrapper.getAssociationType().contains("sample")
|
|
963
|
// ||
|
|
964
|
// associationWrapper.getAssociationType().contains("same
|
|
965
|
// in situ")){
|
|
966
|
if (currentDerivedFrom == null) {
|
|
967
|
state.getReport()
|
|
968
|
.addInfoMessage(String.format(
|
|
969
|
"No derivation event found for unit %s. Defaulting to ACCESSIONING event.",
|
|
970
|
SpecimenImportUtility.getUnitID(currentUnit, config)));
|
|
971
|
DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit,
|
|
972
|
DerivationEventType.ACCESSIONING());
|
|
973
|
} else {
|
|
974
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(
|
|
975
|
associatedUnit, currentUnit, currentDerivedFrom.getType());
|
|
976
|
updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
977
|
updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
978
|
updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
979
|
updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
980
|
|
|
981
|
}
|
|
982
|
state.getReport().addDerivate(associatedUnit, currentUnit, config);
|
|
983
|
// }
|
|
984
|
// siblings relation
|
|
985
|
// connect current unit to field unit of
|
|
986
|
// associated unit
|
|
987
|
// else
|
|
988
|
// if(associationWrapper.getAssociationType().contains("population")||
|
|
989
|
// associationWrapper.getAssociationType().contains("sample")){
|
|
990
|
// //no associated field unit -> using
|
|
991
|
// current one
|
|
992
|
// if(associatedFieldUnit==null){
|
|
993
|
// if(currentFieldUnit!=null){
|
|
994
|
// DerivationEvent.NewSimpleInstance(currentFieldUnit,
|
|
995
|
// associatedUnit,
|
|
996
|
// DerivationEventType.ACCESSIONING());
|
|
997
|
// }
|
|
998
|
// }
|
|
999
|
// else{
|
|
1000
|
// if(currentDerivedFrom==null){
|
|
1001
|
// state.getReport().addInfoMessage("No
|
|
1002
|
// derivation event found for unit
|
|
1003
|
// "+SpecimenImportUtility.getUnitID(currentUnit,
|
|
1004
|
// config)+". Defaulting to ACCESIONING
|
|
1005
|
// event.");
|
|
1006
|
// DerivationEvent.NewSimpleInstance(associatedFieldUnit,
|
|
1007
|
// currentUnit,
|
|
1008
|
// DerivationEventType.ACCESSIONING());
|
|
1009
|
// }
|
|
1010
|
// if(currentDerivedFrom!=null &&
|
|
1011
|
// associatedFieldUnit==currentFieldUnit){
|
|
1012
|
// DerivationEvent updatedDerivationEvent =
|
|
1013
|
// DerivationEvent.NewSimpleInstance(associatedFieldUnit,
|
|
1014
|
// currentUnit,
|
|
1015
|
// currentDerivedFrom.getType());
|
|
1016
|
// updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
1017
|
// updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
1018
|
// updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
1019
|
// updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
1020
|
// }
|
|
1021
|
// }
|
|
1022
|
// }
|
|
1023
|
|
|
1024
|
// delete current field unit if replaced
|
|
1025
|
if (currentFieldUnit != null && currentDerivedFrom != null
|
|
1026
|
&& currentFieldUnit.getDerivationEvents().size() == 1
|
|
1027
|
&& currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) // making
|
|
1028
|
// sure
|
|
1029
|
// that
|
|
1030
|
// the
|
|
1031
|
// field
|
|
1032
|
// unit
|
|
1033
|
&& currentDerivedFrom.getDerivatives().size() == 1
|
|
1034
|
&& currentDerivedFrom.getDerivatives().contains(currentUnit) // is
|
|
1035
|
// not
|
|
1036
|
// attached
|
|
1037
|
// to
|
|
1038
|
// other
|
|
1039
|
// derived
|
|
1040
|
// units
|
|
1041
|
&& currentDerivedFrom != currentUnit.getDerivedFrom() // <-
|
|
1042
|
// derivation
|
|
1043
|
// has
|
|
1044
|
// been
|
|
1045
|
// replaced
|
|
1046
|
// and
|
|
1047
|
// can
|
|
1048
|
// be
|
|
1049
|
// deleted
|
|
1050
|
) {
|
|
1051
|
currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
|
|
1052
|
if (associatedFieldUnit != null && associatedFieldUnit.getGatheringEvent() != null && associatedFieldUnit.getGatheringEvent().getActor() == null && currentFieldUnit.getGatheringEvent().getActor() != null){
|
|
1053
|
associatedFieldUnit.getGatheringEvent().setActor(currentFieldUnit.getGatheringEvent().getActor());
|
|
1054
|
}
|
|
1055
|
if (associatedFieldUnit != null && associatedFieldUnit.getFieldNumber() == null && currentFieldUnit.getFieldNumber() != null) {
|
|
1056
|
associatedFieldUnit.setFieldNumber(currentFieldUnit.getFieldNumber());
|
|
1057
|
}
|
|
1058
|
|
|
1059
|
if (currentFieldUnit.getDerivationEvents().isEmpty()) {
|
|
1060
|
DeleteResult result = state.getCdmRepository().getOccurrenceService()
|
|
1061
|
.delete(currentFieldUnit, deleteConfig);
|
|
1062
|
|
|
1063
|
|
|
1064
|
} else {
|
|
1065
|
|
|
1066
|
logger.debug("there are still derivation events in fieldUnit "
|
|
1067
|
+ currentFieldUnit.getId());
|
|
1068
|
}
|
|
1069
|
|
|
1070
|
}
|
|
1071
|
state.setLastFieldUnit(associatedFieldUnit);
|
|
1072
|
save(associatedUnit, state);
|
|
1073
|
}
|
|
1074
|
}
|
|
1075
|
}
|
|
1076
|
}
|
|
1077
|
}
|
|
1078
|
}
|
|
1079
|
}
|
|
1080
|
// TODO: pop state
|
|
1081
|
state.reset();
|
|
1082
|
state.setDerivedUnitBase(currentUnit);
|
|
1083
|
state.setActualAccessPoint(currentAccessPoint);
|
|
1084
|
state.setPrefix(currentPrefix);
|
|
1085
|
}
|
|
1086
|
|
|
1087
|
private void importAssociatedDna(Abcd206ImportState state, Object itemObject, DerivedUnitFacade derivedUnitFacade) {
|
|
1088
|
URI dnaSource = state.getConfig().getDnaSoure();
|
|
1089
|
String unitId = derivedUnitFacade.getCatalogNumber();
|
|
1090
|
if (unitId == null) {
|
|
1091
|
unitId = derivedUnitFacade.getAccessionNumber();
|
|
1092
|
}
|
|
1093
|
if (unitId == null) {
|
|
1094
|
unitId = derivedUnitFacade.getBarcode();
|
|
1095
|
}
|
|
1096
|
|
|
1097
|
UnitAssociationParser unitParser = new UnitAssociationParser(state.getPrefix(), state.getReport(),
|
|
1098
|
state.getCdmRepository());
|
|
1099
|
UnitAssociationWrapper unitAssociationWrapper = null;
|
|
1100
|
|
|
1101
|
unitAssociationWrapper = unitParser.parseSiblings(unitId, dnaSource);
|
|
1102
|
|
|
1103
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
1104
|
// DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
1105
|
FieldUnit currentFieldUnit = derivedUnitFacade.getFieldUnit(false);
|
|
1106
|
if (unitAssociationWrapper != null) {
|
|
1107
|
NodeList associatedUnits = unitAssociationWrapper.getAssociatedUnits();
|
|
1108
|
if (associatedUnits != null) {
|
|
1109
|
for (int m = 0; m < associatedUnits.getLength(); m++) {
|
|
1110
|
if (associatedUnits.item(m) instanceof Element) {
|
|
1111
|
state.reset();
|
|
1112
|
String associationType = AbcdParseUtility
|
|
1113
|
.parseFirstTextContent(((Element) associatedUnits.item(m))
|
|
1114
|
.getElementsByTagName(unitAssociationWrapper.getPrefix() + "AssociationType"));
|
|
1115
|
Abcd206XMLFieldGetter fieldGetter = new Abcd206XMLFieldGetter(state.getDataHolder(), unitAssociationWrapper.getPrefix());
|
|
1116
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m),
|
|
1117
|
fieldGetter,
|
|
1118
|
state);
|
|
1119
|
// logger.debug("derived unit: " +
|
|
1120
|
// state.getDerivedUnitBase().toString() + " associated
|
|
1121
|
// unit: " +state.getDataHolder().getKindOfUnit() + ", "
|
|
1122
|
// + state.getDataHolder().accessionNumber + ", " +
|
|
1123
|
// state.getDataHolder().getRecordBasis() + ", " +
|
|
1124
|
// state.getDataHolder().getUnitID());
|
|
1125
|
URI lastAccessPoint = state.getActualAccessPoint();
|
|
1126
|
state.setActualAccessPoint(dnaSource);
|
|
1127
|
String oldPrefix = state.getPrefix();
|
|
1128
|
state.setPrefix(unitAssociationWrapper.getPrefix());
|
|
1129
|
handleSingleUnit(state, associatedUnits.item(m), false);
|
|
1130
|
state.setActualAccessPoint(lastAccessPoint);
|
|
1131
|
state.setPrefix(oldPrefix);
|
|
1132
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
1133
|
FieldUnit associatedFieldUnit = null;
|
|
1134
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository()
|
|
1135
|
.getOccurrenceService().findFieldUnits(associatedUnit.getUuid(), null);
|
|
1136
|
// ignore field unit if associated unit has more than
|
|
1137
|
// one
|
|
1138
|
if (associatedFieldUnits.size() > 1) {
|
|
1139
|
state.getReport()
|
|
1140
|
.addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
1141
|
} else if (associatedFieldUnits.size() == 1) {
|
|
1142
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
1143
|
}
|
|
1144
|
// parent-child relation:
|
|
1145
|
if (associationType != null && (associationType.contains("individual")
|
|
1146
|
|| associationType.contains("culture") || associationType.contains("sample")
|
|
1147
|
|| associationType.contains("isolated"))) {
|
|
1148
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(currentUnit,
|
|
1149
|
associatedUnit, DerivationEventType.ACCESSIONING());
|
|
1150
|
|
|
1151
|
updatedDerivationEvent.setDescription(associationType);
|
|
1152
|
if (associatedFieldUnit != null && !associatedFieldUnit.equals(currentFieldUnit) && currentFieldUnit != null) {
|
|
1153
|
associatedFieldUnit.removeDerivationEvent(updatedDerivationEvent);
|
|
1154
|
if ((associatedFieldUnit.getGatheringEvent() != null && associatedFieldUnit.getGatheringEvent().getActor() != null) && (currentFieldUnit.getGatheringEvent() != null && currentFieldUnit.getGatheringEvent().getActor() == null)){
|
|
1155
|
currentFieldUnit.getGatheringEvent().setActor(associatedFieldUnit.getGatheringEvent().getActor());
|
|
1156
|
}
|
|
1157
|
if (associatedFieldUnit.getFieldNumber() != null && currentFieldUnit.getFieldNumber() == null){
|
|
1158
|
currentFieldUnit.setFieldNumber(associatedFieldUnit.getFieldNumber());
|
|
1159
|
}
|
|
1160
|
|
|
1161
|
|
|
1162
|
|
|
1163
|
SpecimenDeleteConfigurator deleteConfig = new SpecimenDeleteConfigurator();
|
|
1164
|
deleteConfig.setDeleteChildren(false);
|
|
1165
|
DeleteResult result = state.getCdmRepository().getOccurrenceService()
|
|
1166
|
.delete(associatedFieldUnit, deleteConfig);
|
|
1167
|
state.setFieldUnit(currentFieldUnit);
|
|
1168
|
|
|
1169
|
// }
|
|
1170
|
if (updatedDerivationEvent.getOriginals().isEmpty()) {
|
|
1171
|
// state.getCdmRepository().getOccurrenceService().deleteDerivationEvent(updatedDerivationEvent);
|
|
1172
|
}
|
|
1173
|
}else{
|
|
1174
|
state.setLastFieldUnit(associatedFieldUnit);
|
|
1175
|
}
|
|
1176
|
state.getReport().addDerivate(associatedUnit, currentUnit, state.getConfig());
|
|
1177
|
}
|
|
1178
|
save(associatedUnit, state);
|
|
1179
|
|
|
1180
|
}
|
|
1181
|
}
|
|
1182
|
}
|
|
1183
|
}
|
|
1184
|
state.reset();
|
|
1185
|
state.setDerivedUnitBase(currentUnit);
|
|
1186
|
|
|
1187
|
}
|
|
1188
|
|
|
1189
|
/**
|
|
1190
|
* @param derivedUnitFacade
|
|
1191
|
* @param sour
|
|
1192
|
* @return
|
|
1193
|
*/
|
|
1194
|
private boolean sourceNotLinkedToElement(DerivedUnitFacade derivedUnitFacade, OriginalSourceBase source) {
|
|
1195
|
Set<IdentifiableSource> linkedSources = derivedUnitFacade.getSources();
|
|
1196
|
for (IdentifiableSource is : linkedSources) {
|
|
1197
|
if (is.getCitation() != null && source.getCitation() != null
|
|
1198
|
&& is.getCitation().getTitleCache().equalsIgnoreCase(source.getCitation().getTitleCache())) {
|
|
1199
|
String isDetail = is.getCitationMicroReference();
|
|
1200
|
if ((StringUtils.isBlank(isDetail) && StringUtils.isBlank(source.getCitationMicroReference()))
|
|
1201
|
|| (isDetail != null && isDetail.equalsIgnoreCase(source.getCitationMicroReference()))) {
|
|
1202
|
return false;
|
|
1203
|
}
|
|
1204
|
}
|
|
1205
|
}
|
|
1206
|
return true;
|
|
1207
|
}
|
|
1208
|
|
|
1209
|
|
|
1210
|
|
|
1211
|
/**
|
|
1212
|
* setCollectionData : store the collection object into the
|
|
1213
|
* derivedUnitFacade
|
|
1214
|
*
|
|
1215
|
* @param state
|
|
1216
|
*/
|
|
1217
|
protected void setCollectionData(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
|
|
1218
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
1219
|
SpecimenImportUtility.setUnitID(derivedUnitFacade.innerDerivedUnit(), state.getDataHolder().getUnitID(),
|
|
1220
|
config);
|
|
1221
|
if (!config.isMapUnitIdToAccessionNumber()) {
|
|
1222
|
derivedUnitFacade.setAccessionNumber(NB(state.getDataHolder().accessionNumber));
|
|
1223
|
}
|
|
1224
|
// derivedUnitFacade.setCollectorsNumber(NB(state.getDataHolder().collectorsNumber));
|
|
1225
|
|
|
1226
|
/*
|
|
1227
|
* INSTITUTION & COLLECTION
|
|
1228
|
*/
|
|
1229
|
// manage institution
|
|
1230
|
Institution institution = this.getInstitution(NB(state.getDataHolder().institutionCode), state);
|
|
1231
|
// manage collection
|
|
1232
|
Collection collection = this.getCollection(institution, NB(state.getDataHolder().collectionCode), state);
|
|
1233
|
// link specimen & collection
|
|
1234
|
derivedUnitFacade.setCollection(collection);
|
|
1235
|
}
|
|
1236
|
|
|
1237
|
/**
|
|
1238
|
* getFacade : get the DerivedUnitFacade based on the recordBasis
|
|
1239
|
*
|
|
1240
|
* @param state
|
|
1241
|
*
|
|
1242
|
* @return DerivedUnitFacade
|
|
1243
|
*/
|
|
1244
|
@Override
|
|
1245
|
protected DerivedUnitFacade getFacade(Abcd206ImportState state) {
|
|
1246
|
if (logger.isDebugEnabled()) {
|
|
1247
|
logger.info("getFacade()");
|
|
1248
|
}
|
|
1249
|
SpecimenOrObservationType type = null;
|
|
1250
|
DefinedTerm kindOfUnit = null;
|
|
1251
|
|
|
1252
|
// create specimen
|
|
1253
|
if (NB((state.getDataHolder()).getRecordBasis()) != null) {
|
|
1254
|
if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living") > -1) {
|
|
1255
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
1256
|
} else if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s")
|
|
1257
|
|| state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen") > -1) {// specimen
|
|
1258
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
1259
|
} else if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o")
|
|
1260
|
|| state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation") > -1) {
|
|
1261
|
if (state.getDataHolder().getRecordBasis().toLowerCase().contains("machine")
|
|
1262
|
&& state.getDataHolder().getRecordBasis().toLowerCase().contains("observation")) {
|
|
1263
|
type = SpecimenOrObservationType.MachineObservation;
|
|
1264
|
} else if (state.getDataHolder().getRecordBasis().toLowerCase().contains("human")
|
|
1265
|
&& state.getDataHolder().getRecordBasis().toLowerCase().contains("observation")) {
|
|
1266
|
type = SpecimenOrObservationType.HumanObservation;
|
|
1267
|
} else {
|
|
1268
|
type = SpecimenOrObservationType.Observation;
|
|
1269
|
}
|
|
1270
|
} else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil") > -1) {
|
|
1271
|
type = SpecimenOrObservationType.Fossil;
|
|
1272
|
} else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("materialsample") > -1) {
|
|
1273
|
type = SpecimenOrObservationType.MaterialSample;
|
|
1274
|
} else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("sample") > -1) {
|
|
1275
|
type = SpecimenOrObservationType.TissueSample;
|
|
1276
|
}
|
|
1277
|
|
|
1278
|
if (type == null) {
|
|
1279
|
logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
|
|
1280
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
1281
|
}
|
|
1282
|
} else {
|
|
1283
|
logger.info("The basis of record is null");
|
|
1284
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
1285
|
}
|
|
1286
|
|
|
1287
|
if (NB((state.getDataHolder()).getKindOfUnit()) != null) {
|
|
1288
|
kindOfUnit = getKindOfUnit(state, null, state.getDataHolder().getKindOfUnit().toLowerCase(), null, null,
|
|
1289
|
null);
|
|
1290
|
if (kindOfUnit == null) {
|
|
1291
|
if (state.getDataHolder().getKindOfUnit().toLowerCase().indexOf("clone") > -1) {
|
|
1292
|
kindOfUnit = getKindOfUnit(state, null, "clone culture", "clone culture", "cc", null);
|
|
1293
|
} else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("live")) {
|
|
1294
|
kindOfUnit = getKindOfUnit(state, null, "live sample", "live sample", "ls", null);
|
|
1295
|
} else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("microscopic slide")) {
|
|
1296
|
kindOfUnit = getKindOfUnit(state, null, "microscopic slide", "microscopic slide", "ms", null);
|
|
1297
|
}
|
|
1298
|
|
|
1299
|
if (kindOfUnit == null) {
|
|
1300
|
logger.info("The kind of unit does not seem to be known: " + state.getDataHolder().getKindOfUnit());
|
|
1301
|
|
|
1302
|
}
|
|
1303
|
}
|
|
1304
|
} else {
|
|
1305
|
logger.info("The kind of unit is null");
|
|
1306
|
|
|
1307
|
}
|
|
1308
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
1309
|
derivedUnitFacade.setFieldUnit(state.getFieldUnit(state.getDataHolder().getFieldNumber()));
|
|
1310
|
derivedUnitFacade.setDerivedUnitKindOfUnit(kindOfUnit);
|
|
1311
|
derivedUnitFacade.setPreferredStableUri(state.getDataHolder().getPreferredStableUri());
|
|
1312
|
// derivedUnitFacade.setDerivedUnitKindOfUnit(kindOfUnit);
|
|
1313
|
return derivedUnitFacade;
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
private void getCollectorsFromXML(Element root, Abcd206XMLFieldGetter abcdFieldGetter, Abcd206ImportState state) {
|
|
1317
|
NodeList group;
|
|
1318
|
|
|
1319
|
group = root.getChildNodes();
|
|
1320
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1321
|
if (group.item(i).getNodeName().equals(state.getPrefix() + "Identifications")) {
|
|
1322
|
group = group.item(i).getChildNodes();
|
|
1323
|
break;
|
|
1324
|
}
|
|
1325
|
}
|
|
1326
|
// state.getDataHolder().gatheringAgents = "";
|
|
1327
|
|
|
1328
|
abcdFieldGetter.getType(root);
|
|
1329
|
abcdFieldGetter.getGatheringPeople(root);
|
|
1330
|
}
|
|
1331
|
|
|
1332
|
|
|
1333
|
/**
|
|
1334
|
* Load the list of names from the ABCD file and save them
|
|
1335
|
*
|
|
1336
|
* @param state
|
|
1337
|
* : the current ABCD import state
|
|
1338
|
* @param unitsList
|
|
1339
|
* : the unit list from the ABCD file
|
|
1340
|
* @param abcdFieldGetter
|
|
1341
|
* : the ABCD parser
|
|
1342
|
*/
|
|
1343
|
private void prepareCollectors(Abcd206ImportState state, NodeList unitsList,
|
|
1344
|
Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
1345
|
|
|
1346
|
TeamOrPersonBase<?> teamOrPerson = null;
|
|
1347
|
Team team = null;
|
|
1348
|
// ImportHelper.setOriginalSource(teamOrPerson,
|
|
1349
|
// state.getConfig().getSourceReference(), collector, "Collector");
|
|
1350
|
for (int i = 0; i < unitsList.getLength(); i++) {
|
|
1351
|
this.getCollectorsFromXML((Element) unitsList.item(i), abcdFieldGetter, state);
|
|
1352
|
if (!(state.getDataHolder().gatheringAgentsList.isEmpty())) {
|
|
1353
|
if (state.getDataHolder().gatheringAgentsList.size() == 1) {
|
|
1354
|
teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgentsList.get(0));
|
|
1355
|
} else {
|
|
1356
|
team = new Team();
|
|
1357
|
for (String collector : state.getDataHolder().gatheringAgentsList) {
|
|
1358
|
teamOrPerson = parseAuthorString(collector);
|
|
1359
|
if (teamOrPerson instanceof Person) {
|
|
1360
|
team.addTeamMember((Person) teamOrPerson);
|
|
1361
|
} else {
|
|
1362
|
for (Person person : ((Team) teamOrPerson).getTeamMembers()) {
|
|
1363
|
team.addTeamMember(person);
|
|
1364
|
}
|
|
1365
|
}
|
|
1366
|
}
|
|
1367
|
if (team.getTeamMembers() != null && team.getTeamMembers().isEmpty()){
|
|
1368
|
teamOrPerson = team;
|
|
1369
|
}
|
|
1370
|
}
|
|
1371
|
if (!state.getPersonStore().containsId(teamOrPerson.getTitleCache())) {
|
|
1372
|
state.getPersonStore().put(teamOrPerson.getTitleCache(), teamOrPerson);
|
|
1373
|
if (logger.isDebugEnabled()) {
|
|
1374
|
logger.debug("Stored author " + state.getDataHolder().gatheringAgentsList.toString());
|
|
1375
|
}
|
|
1376
|
logger.warn("Not imported author with duplicated aut_id "
|
|
1377
|
+ state.getDataHolder().gatheringAgentsList.toString());
|
|
1378
|
}
|
|
1379
|
}
|
|
1380
|
if (!StringUtils.isBlank(state.getDataHolder().gatheringAgentsText)
|
|
1381
|
&& state.getDataHolder().gatheringAgentsList.isEmpty()) {
|
|
1382
|
teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgentsText);
|
|
1383
|
// if (teamOrPerson instanceof Person) {
|
|
1384
|
// //team.addTeamMember((Person) teamOrPerson);
|
|
1385
|
// } else {
|
|
1386
|
// team = new Team();
|
|
1387
|
// for (Person person : ((Team) teamOrPerson).getTeamMembers())
|
|
1388
|
// {
|
|
1389
|
// team.addTeamMember(person);
|
|
1390
|
// }
|
|
1391
|
// }
|
|
1392
|
if (!state.getPersonStore().containsId(teamOrPerson.getTitleCache())) {
|
|
1393
|
state.getPersonStore().put(teamOrPerson.getTitleCache(), teamOrPerson);
|
|
1394
|
if (logger.isDebugEnabled()) {
|
|
1395
|
logger.debug("Stored author " + state.getDataHolder().gatheringAgentsText);
|
|
1396
|
}
|
|
1397
|
logger.warn("Not imported author with duplicated aut_id "
|
|
1398
|
+ state.getDataHolder().gatheringAgentsList.toString());
|
|
1399
|
}
|
|
1400
|
}
|
|
1401
|
|
|
1402
|
}
|
|
1403
|
|
|
1404
|
// List<String> collectorsU = new ArrayList<String>(new
|
|
1405
|
// HashSet<String>(collectors));
|
|
1406
|
// List<String> teamsU = new ArrayList<String>(new
|
|
1407
|
// HashSet<String>(teams));
|
|
1408
|
//
|
|
1409
|
//
|
|
1410
|
// //existing teams in DB
|
|
1411
|
// Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
|
|
1412
|
// List<UuidAndTitleCache<Team>> hiberTeam = new
|
|
1413
|
// ArrayList<UuidAndTitleCache<Team>>();//getAgentService().getTeamUuidAndTitleCache();
|
|
1414
|
|
|
1415
|
// Set<UUID> uuids = new HashSet<UUID>();
|
|
1416
|
// for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
|
|
1417
|
// uuids.add(hibernateT.getUuid());
|
|
1418
|
// }
|
|
1419
|
// if (!uuids.isEmpty()){
|
|
1420
|
// List<AgentBase> existingTeams = getAgentService().find(uuids);
|
|
1421
|
// for (AgentBase<?> existingP:existingTeams){
|
|
1422
|
// titleCacheTeam.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Team.class));
|
|
1423
|
// }
|
|
1424
|
// }
|
|
1425
|
|
|
1426
|
// Map<String,UUID> teamMap = new HashMap<String, UUID>();
|
|
1427
|
// for (UuidAndTitleCache<Team> uuidt:hiberTeam){
|
|
1428
|
// teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
|
|
1429
|
// }
|
|
1430
|
|
|
1431
|
// existing persons in DB
|
|
1432
|
// List<UuidAndTitleCache<Person>> hiberPersons = new
|
|
1433
|
// ArrayList<UuidAndTitleCache<Person>>();//getAgentService().getPersonUuidAndTitleCache();
|
|
1434
|
// Map<String,Person> titleCachePerson = new HashMap<String, Person>();
|
|
1435
|
// uuids = new HashSet<UUID>();
|
|
1436
|
// for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
1437
|
// uuids.add(hibernateP.getUuid());
|
|
1438
|
// }
|
|
1439
|
//
|
|
1440
|
// if (!uuids.isEmpty()){
|
|
1441
|
// List<AgentBase> existingPersons = getAgentService().find(uuids);
|
|
1442
|
// for (AgentBase<?> existingP:existingPersons){
|
|
1443
|
// titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Person.class));
|
|
1444
|
// }
|
|
1445
|
// }
|
|
1446
|
//
|
|
1447
|
// Map<String,UUID> personMap = new HashMap<String, UUID>();
|
|
1448
|
// for (UuidAndTitleCache<Person> person:hiberPersons){
|
|
1449
|
// personMap.put(person.getTitleCache(), person.getUuid());
|
|
1450
|
// }
|
|
1451
|
//
|
|
1452
|
// java.util.Collection<Person> personToadd = new ArrayList<Person>();
|
|
1453
|
// java.util.Collection<Team> teamToAdd = new ArrayList<Team>();
|
|
1454
|
//
|
|
1455
|
// for (String collector:collectorsU){
|
|
1456
|
// Person p = Person.NewInstance();
|
|
1457
|
// p.setTitleCache(collector,true);
|
|
1458
|
// if (!personMap.containsKey(p.getTitleCache())){
|
|
1459
|
// personToadd.add(p);
|
|
1460
|
// }
|
|
1461
|
// }
|
|
1462
|
// for (String team:teamsU){
|
|
1463
|
// Team p = Team.NewInstance();
|
|
1464
|
// p.setTitleCache(team,true);
|
|
1465
|
// if (!teamMap.containsKey(p.getTitleCache())){
|
|
1466
|
// teamToAdd.add(p);
|
|
1467
|
// }
|
|
1468
|
// }
|
|
1469
|
//
|
|
1470
|
// if(!personToadd.isEmpty()){
|
|
1471
|
// for (Person agent: personToadd){
|
|
1472
|
// save(agent, state);
|
|
1473
|
// titleCachePerson.put(agent.getTitleCache(),CdmBase.deproxy(agent,
|
|
1474
|
// Person.class) );
|
|
1475
|
// }
|
|
1476
|
// }
|
|
1477
|
//
|
|
1478
|
// Person ptmp ;
|
|
1479
|
// Map <String,Integer>teamdone = new HashMap<String, Integer>();
|
|
1480
|
// for (List<String> collteam: collectorinteams){
|
|
1481
|
// if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
|
|
1482
|
// Team team = new Team();
|
|
1483
|
// boolean em =true;
|
|
1484
|
// for (String collector:collteam){
|
|
1485
|
// ptmp = Person.NewInstance();
|
|
1486
|
// ptmp.setTitleCache(collector,true);
|
|
1487
|
// Person p2 = titleCachePerson.get(ptmp.getTitleCache());
|
|
1488
|
// team.addTeamMember(p2);
|
|
1489
|
// em=false;
|
|
1490
|
// }
|
|
1491
|
// if (!em) {
|
|
1492
|
// teamToAdd.add(team);
|
|
1493
|
// }
|
|
1494
|
// teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
|
|
1495
|
// }
|
|
1496
|
// }
|
|
1497
|
//
|
|
1498
|
// if(!teamToAdd.isEmpty()){
|
|
1499
|
// for (Team agent: teamToAdd){
|
|
1500
|
// save(agent, state);
|
|
1501
|
// titleCacheTeam.put(agent.getTitleCache(), CdmBase.deproxy(
|
|
1502
|
// agent,Team.class) );
|
|
1503
|
// }
|
|
1504
|
// }
|
|
1505
|
|
|
1506
|
// ((Abcd206ImportConfigurator)
|
|
1507
|
// state.getConfig()).setTeams(titleCacheTeam);
|
|
1508
|
// ((Abcd206ImportConfigurator)
|
|
1509
|
// state.getConfig()).setPersons(titleCachePerson);
|
|
1510
|
}
|
|
1511
|
|
|
1512
|
@Override
|
|
1513
|
protected boolean doCheck(Abcd206ImportState state) {
|
|
1514
|
logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
|
|
1515
|
return true;
|
|
1516
|
}
|
|
1517
|
|
|
1518
|
@Override
|
|
1519
|
protected boolean isIgnore(Abcd206ImportState state) {
|
|
1520
|
return false;
|
|
1521
|
}
|
|
1522
|
|
|
1523
|
@Override
|
|
1524
|
protected DefinedTerm getKindOfUnit(Abcd206ImportState state, UUID uuid, String label, String description,
|
|
1525
|
String labelAbbrev, TermVocabulary<DefinedTerm> voc) {
|
|
1526
|
|
|
1527
|
DefinedTerm unit = null;
|
|
1528
|
|
|
1529
|
if (uuid == null) {
|
|
1530
|
unit = this.kindOfUnitsMap.get(label.toLowerCase());
|
|
1531
|
} else {
|
|
1532
|
unit = state.getKindOfUnit(uuid);
|
|
1533
|
|
|
1534
|
}
|
|
1535
|
if (unit == null) {
|
|
1536
|
unit = (DefinedTerm) getTermService().find(uuid);
|
|
1537
|
if (unit == null) {
|
|
1538
|
if (uuid == null) {
|
|
1539
|
uuid = UUID.randomUUID();
|
|
1540
|
}
|
|
1541
|
unit = DefinedTerm.NewKindOfUnitInstance(description, label, labelAbbrev);
|
|
1542
|
unit.setUuid(uuid);
|
|
1543
|
if (voc == null) {
|
|
1544
|
boolean isOrdered = false;
|
|
1545
|
voc = getVocabulary(state, TermType.KindOfUnit, uuidUserDefinedKindOfUnitVocabulary,
|
|
1546
|
"User defined vocabulary for kind-of-units", "User Defined Measurement kind-of-units", null,
|
|
1547
|
null, isOrdered, unit);
|
|
1548
|
}
|
|
1549
|
voc.addTerm(unit);
|
|
1550
|
getTermService().save(unit);
|
|
1551
|
}
|
|
1552
|
state.putKindOfUnit(unit);
|
|
1553
|
kindOfUnitsMap.put(unit.getLabel().toLowerCase(), unit);
|
|
1554
|
}
|
|
1555
|
return unit;
|
|
1556
|
}
|
|
1557
|
|
|
1558
|
|
|
1559
|
|
|
1560
|
}
|