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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.sdd.in;
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import java.io.File;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.joda.time.DateTime;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.IDescriptionService;
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import eu.etaxonomy.cdm.common.mediaMetaData.ImageMetaData;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.ICdmImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.sdd.SDDTransformer;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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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.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.common.TermBase;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.VersionableEntity;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.Modifier;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
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import eu.etaxonomy.cdm.model.media.ImageFile;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.Specimen;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
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/**
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* @author h.fradin
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* @created 24.10.2008
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* @version 1.0
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*/
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@Component("sddImport")
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public class SDDImport extends CdmImportBase<SDDImportConfigurator, SDDImportState> implements ICdmImport<SDDImportConfigurator, SDDImportState> {
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private static final Logger logger = Logger.getLogger(SDDImport.class);
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private static int modCount = 1000;
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private Map<String,Person> authors = new HashMap<String,Person>();
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private Map<String,String> citations = new HashMap<String,String>();
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private Map<String,String> defaultUnitPrefixes = new HashMap<String,String>();
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private Map<String,Person> editors = new HashMap<String,Person>();
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private Map<String,FeatureNode> featureNodes = new HashMap<String,FeatureNode>();
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private Map<String,Feature> features = new HashMap<String,Feature>();
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private Map<String,String> locations = new HashMap<String,String>();
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private Map<String,List<CdmBase>> mediaObject_ListCdmBase = new HashMap<String,List<CdmBase>>();
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private Map<String,String> mediaObject_Role = new HashMap<String,String>();
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private Map<String,ReferenceBase> publications = new HashMap<String,ReferenceBase>();
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private Map<String,State> states = new HashMap<String,State>();
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private Map<String,TaxonDescription> taxonDescriptions = new HashMap<String,TaxonDescription>();
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private Map<String,NonViralName> taxonNameBases = new HashMap<String,NonViralName>();
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private Map<String,MeasurementUnit> units = new HashMap<String,MeasurementUnit>();
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private Map<String,TaxonNode> taxonNodes = new HashMap<String,TaxonNode>();
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private Map<String,NamedArea> namedAreas = new HashMap<String,NamedArea>();
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private Map<String,Specimen> specimens = new HashMap<String,Specimen>();
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private Map<String,Modifier> modifiers = new HashMap<String,Modifier>();
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private Set<MarkerType> markerTypes = new HashSet<MarkerType>();
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private Set<Feature> descriptiveConcepts = new HashSet<Feature>();
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private Set<AnnotationType> annotationTypes = new HashSet<AnnotationType>();
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private Set<Feature> featureSet = new HashSet<Feature>();
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private ReferenceBase sec = ReferenceFactory.newDatabase();
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private ReferenceBase sourceReference = null;
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private Language datasetLanguage = null;
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private Namespace xmlNamespace = Namespace.getNamespace("xml","http://www.w3.org/XML/1998/namespace");
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private String generatorName = "";
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private String generatorVersion = "";
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private Set<StatisticalMeasure> statisticalMeasures = new HashSet<StatisticalMeasure>();
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private Set<VersionableEntity> featureData = new HashSet<VersionableEntity>();
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private Set<FeatureTree> featureTrees = new HashSet<FeatureTree>();
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private Set<TaxonomicTree> taxonomicTrees = new HashSet<TaxonomicTree>();
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private Rights copyright = null;
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private int taxonNamesCount = 0; //XIM ajout
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public SDDImport(){
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super();
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}
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@Override
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public boolean doCheck(SDDImportState state){
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boolean result = true;
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logger.warn("No check implemented for SDD");
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return result;
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}
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// @Override
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// public boolean doInvoke(IImportConfigurator config, Map<String, MapWrapper<? extends CdmBase>> stores){
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@Override
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public boolean doInvoke(SDDImportState state){
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boolean success = true;
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TransactionStatus ts = startTransaction();
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SDDImportConfigurator sddConfig = state.getConfig();
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logger.info("start Datasets ...");
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// <Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://rs.tdwg.org/UBIF/2006/" xsi:schemaLocation="http://rs.tdwg.org/UBIF/2006/ ../SDD.xsd">
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Element root = sddConfig.getSourceRoot();
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Namespace sddNamespace = sddConfig.getSddNamespace();
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logger.info("start TechnicalMetadata ...");
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// <TechnicalMetadata created="2006-04-20T10:00:00">
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importTechnicalMetadata(root, sddNamespace, sddConfig);
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List<Element> elDatasets = root.getChildren("Dataset",sddNamespace);
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int i = 0;
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//for each Dataset
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logger.info("start Dataset ...");
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for (Element elDataset : elDatasets){
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success &= importDataset(elDataset, sddNamespace, state);
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if ((++i % modCount) == 0){ logger.info("Datasets handled: " + i);}
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logger.info(i + " Datasets handled");
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}
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commitTransaction(ts);
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return success;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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protected boolean isIgnore(SDDImportState state){
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return false;
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}
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// associates the reference of a media object in SDD with a CdmBase Object
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protected void associateImageWithCdmBase(String refMO, CdmBase cb){
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if ((refMO != null) && (cb!=null)) {
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if (! refMO.equals("")) {
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if (! mediaObject_ListCdmBase.containsKey(refMO)) {
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List<CdmBase> lcb = new ArrayList<CdmBase>();
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lcb.add(cb);
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mediaObject_ListCdmBase.put(refMO,lcb);
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} else {
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List<CdmBase> lcb = mediaObject_ListCdmBase.get(refMO);
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lcb.add(cb);
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mediaObject_ListCdmBase.put(refMO,lcb);
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}
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}
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}
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}
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// imports information about the Dataset
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protected void importDatasetRepresentation(Element parent, Namespace sddNamespace){
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logger.info("start Representation ...");
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/* <Representation>
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<Label>The Genus Viola</Label>
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<Detail>This is an example for a very simple SDD file, representing a single description with categorical, quantitative, and text character. Compare also the "Fragment*" examples, which contain more complex examples in the form of document fragments. Intended for version="SDD 1.1".</Detail>
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</Representation>
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*/
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Element elRepresentation = parent.getChild("Representation",sddNamespace);
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String label = (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace);
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String detail = (String)ImportHelper.getXmlInputValue(elRepresentation, "Detail",sddNamespace);
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sec.setTitleCache(label, true);
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if (detail != null) {
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Annotation annotation = Annotation.NewInstance(detail, datasetLanguage);
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annotation.setAnnotationType(AnnotationType.EDITORIAL());
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sec.addAnnotation(annotation);
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}
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List<Element> listMediaObjects = elRepresentation.getChildren("MediaObject",sddNamespace);
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for (Element elMediaObject : listMediaObjects) {
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String ref = null;
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String role = null;
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if (elMediaObject != null) {
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ref = elMediaObject.getAttributeValue("ref");
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role = elMediaObject.getAttributeValue("role");
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}
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if (ref != null) {
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if (!ref.equals("")) {
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this.associateImageWithCdmBase(ref,sourceReference);
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this.associateImageWithCdmBase(ref,sec);
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mediaObject_Role.put(ref,role);
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}
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}
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}
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}
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// imports the representation (label, detail, lang) of a particular SDD element
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protected void importRepresentation(Element parent, Namespace sddNamespace, VersionableEntity ve, String id, IImportConfigurator config){
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Element elRepresentation = parent.getChild("Representation",sddNamespace);
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Map<Language,List<String>> langLabDet = new HashMap<Language,List<String>>();
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handleRepresentationLabels(sddNamespace, elRepresentation, langLabDet);
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handleRepresentationDetails(sddNamespace, elRepresentation, langLabDet);
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if (ve instanceof TermBase) {
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makeRepresentationForTerms((TermBase)ve, langLabDet);
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}else if (ve instanceof Media) {
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makeRepresentationForMedia((Media)ve, langLabDet);
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}else if (ve instanceof IdentifiableEntity<?>) {
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IdentifiableEntity<?> ie = (IdentifiableEntity<?>)ve;
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makeRepresentationForIdentifiableEntity(sddNamespace, ie, elRepresentation, langLabDet);
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if (ve instanceof IdentifiableMediaEntity<?>){
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makeRepresentationForIdentifiableMediaEntity(parent, sddNamespace, (IdentifiableMediaEntity<?>)ve);
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}
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}
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makeRepresentationMediaObjects(sddNamespace, ve, elRepresentation);
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}
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/**
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* Handles the "Detail" children of representations. Adds the result to the langLabDet.
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* @param sddNamespace
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* @param elRepresentation
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* @param langLabDet
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*/
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private void handleRepresentationDetails(Namespace sddNamespace,
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Element elRepresentation, Map<Language, List<String>> langLabDet) {
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List<Element> listDetails = elRepresentation.getChildren("Detail",sddNamespace);
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for (Element elDetail : listDetails){
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Language language = getLanguage(elDetail);
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String role = elDetail.getAttributeValue("role");
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String detail = elDetail.getText();
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List<String> labDet = langLabDet.get(language);
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labDet.add(detail);
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labDet.add(role);
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langLabDet.put(language, labDet);
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}
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}
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/**
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* Handles the "Label" children of representations. Adds the result to the langLabDet.
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* @param sddNamespace
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* @param elRepresentation
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* @param langLabDet
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*/
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private void handleRepresentationLabels(Namespace sddNamespace,
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Element elRepresentation, Map<Language, List<String>> langLabDet) {
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// <Label xml:lang="la">Viola hederacea Labill.</Label>
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List<Element> listLabels = elRepresentation.getChildren("Label",sddNamespace);
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for (Element elLabel : listLabels){
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Language language = getLanguage(elLabel);
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String label = elLabel.getText();
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List<String> labDet = new ArrayList<String>(3);
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labDet.add(label);
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langLabDet.put(language, labDet);
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}
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}
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/**
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*
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* @param ve
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* @param langLabDet
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*/
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private void makeRepresentationForMedia(Media m, Map<Language, List<String>> langLabDet) {
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for (Language lang : langLabDet.keySet()){
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List<String> labDet = langLabDet.get(lang);
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if (labDet.get(0) != null){
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m.addTitle(LanguageString.NewInstance(labDet.get(0), lang));
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}
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if (labDet.size()>1) {
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m.addDescription(labDet.get(1), lang);
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}
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}
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}
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/**
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* Handles representations for terms. Adds one representation per language in langLabDet.
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*
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* @param ve
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* @param langLabDet
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*/
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334
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private void makeRepresentationForTerms(TermBase tb, Map<Language, List<String>> langLabDet) {
|
|
335
|
for (Language lang : langLabDet.keySet()){
|
|
336
|
List<String> labDet = langLabDet.get(lang);
|
|
337
|
if (labDet.size()>0){
|
|
338
|
if (labDet.size()>1) {
|
|
339
|
tb.addRepresentation(Representation.NewInstance(labDet.get(1), labDet.get(0), labDet.get(0), lang));
|
|
340
|
} else {
|
|
341
|
tb.addRepresentation(Representation.NewInstance(labDet.get(0), labDet.get(0), labDet.get(0), lang));
|
|
342
|
}
|
|
343
|
}
|
|
344
|
}
|
|
345
|
}
|
|
346
|
|
|
347
|
|
|
348
|
/**
|
|
349
|
* Handles the "MediaObject" children of representations.
|
|
350
|
* @param sddNamespace
|
|
351
|
* @param ve
|
|
352
|
* @param elRepresentation
|
|
353
|
*/
|
|
354
|
private void makeRepresentationMediaObjects(Namespace sddNamespace,
|
|
355
|
VersionableEntity ve, Element elRepresentation) {
|
|
356
|
List <Element> listMediaObjects = elRepresentation.getChildren("MediaObject", sddNamespace);
|
|
357
|
for (Element elMediaObject : listMediaObjects) {
|
|
358
|
String ref = null;
|
|
359
|
//TODO
|
|
360
|
String role = null;
|
|
361
|
if (elMediaObject != null) {
|
|
362
|
ref = elMediaObject.getAttributeValue("ref");
|
|
363
|
role = elMediaObject.getAttributeValue("role");
|
|
364
|
}
|
|
365
|
if (StringUtils.isNotBlank(ref)) {
|
|
366
|
if (ve instanceof TaxonDescription) {
|
|
367
|
TaxonDescription td = (TaxonDescription) ve;
|
|
368
|
//TODO: ensure that all images are imported
|
|
369
|
if (td.getDescriptionSources().size() > 0) {
|
|
370
|
this.associateImageWithCdmBase(ref,(ReferenceBase) td.getDescriptionSources().toArray()[0]);
|
|
371
|
} else {
|
|
372
|
ReferenceBase descriptionSource = ReferenceFactory.newGeneric();
|
|
373
|
td.addDescriptionSource(descriptionSource);
|
|
374
|
this.associateImageWithCdmBase(ref,descriptionSource);
|
|
375
|
}
|
|
376
|
} else {
|
|
377
|
this.associateImageWithCdmBase(ref,ve);
|
|
378
|
}
|
|
379
|
}
|
|
380
|
}
|
|
381
|
}
|
|
382
|
|
|
383
|
/**
|
|
384
|
* Handles the "Links" element
|
|
385
|
* @param parent
|
|
386
|
* @param sddNamespace
|
|
387
|
* @param ve
|
|
388
|
*/
|
|
389
|
private void makeRepresentationForIdentifiableMediaEntity(Element parent,
|
|
390
|
Namespace sddNamespace, IdentifiableMediaEntity ime) {
|
|
391
|
Element elLinks = parent.getChild("Links",sddNamespace);
|
|
392
|
|
|
393
|
if (elLinks != null) {
|
|
394
|
|
|
395
|
// <Link rel="Alternate" href="http://www.diversitycampus.net/people/hagedorn"/>
|
|
396
|
List<Element> listLinks = elLinks.getChildren("Link", sddNamespace);
|
|
397
|
Media link = Media.NewInstance();
|
|
398
|
MediaRepresentation mr = MediaRepresentation.NewInstance();
|
|
399
|
int k = 0;
|
|
400
|
//for each Link
|
|
401
|
for (Element elLink : listLinks){
|
|
402
|
|
|
403
|
try {
|
|
404
|
//TODO
|
|
405
|
String rel = elLink.getAttributeValue("rel");
|
|
406
|
String href = elLink.getAttributeValue("href");
|
|
407
|
|
|
408
|
mr.addRepresentationPart(MediaRepresentationPart.NewInstance(href, null));
|
|
409
|
link.addRepresentation(mr);
|
|
410
|
ime.addMedia(link);
|
|
411
|
|
|
412
|
} catch (Exception e) {
|
|
413
|
//FIXME
|
|
414
|
logger.warn("Import of Link " + k + " failed.");
|
|
415
|
}
|
|
416
|
|
|
417
|
if ((++k % modCount) == 0){ logger.info("Links handled: " + k);}
|
|
418
|
|
|
419
|
}
|
|
420
|
}
|
|
421
|
}
|
|
422
|
|
|
423
|
/**
|
|
424
|
* @param sddNamespace
|
|
425
|
* @param ve
|
|
426
|
* @param elRepresentation
|
|
427
|
* @param langLabDet
|
|
428
|
* @return
|
|
429
|
*/
|
|
430
|
private void makeRepresentationForIdentifiableEntity(Namespace sddNamespace, IdentifiableEntity<?> ie,
|
|
431
|
Element elRepresentation, Map<Language, List<String>> langLabDet) {
|
|
432
|
List<String> labDet = null;
|
|
433
|
|
|
434
|
if (ie instanceof TaxonNameBase) {
|
|
435
|
if (langLabDet.keySet().contains(getTermService().getLanguageByIso("la"))) {
|
|
436
|
labDet = langLabDet.get(getTermService().getLanguageByIso("la"));
|
|
437
|
} else if (langLabDet.keySet().contains(datasetLanguage)) {
|
|
438
|
labDet = langLabDet.get(datasetLanguage);
|
|
439
|
logger.info("TaxonName " + (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace) + " is not specified as a latin name.");
|
|
440
|
} else {
|
|
441
|
labDet = langLabDet.get(langLabDet.keySet().iterator().next());
|
|
442
|
logger.info("TaxonName " + (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace) + " is not specified as a latin name.");
|
|
443
|
}
|
|
444
|
} else {
|
|
445
|
labDet = langLabDet.get(langLabDet.keySet().iterator().next());
|
|
446
|
}
|
|
447
|
|
|
448
|
//FIXME labDet is != null only for TaxonNameBase
|
|
449
|
ie.setTitleCache(labDet.get(0), true);
|
|
450
|
|
|
451
|
if (labDet.size()>1) {
|
|
452
|
Annotation annotation = null;
|
|
453
|
if (labDet.get(1) != null) {
|
|
454
|
if (labDet.get(2) != null) {
|
|
455
|
annotation = Annotation.NewInstance(labDet.get(2) + " - " + labDet.get(1), datasetLanguage);
|
|
456
|
} else {
|
|
457
|
annotation = Annotation.NewInstance(labDet.get(1), datasetLanguage);
|
|
458
|
}
|
|
459
|
}
|
|
460
|
ie.addAnnotation(annotation);
|
|
461
|
}
|
|
462
|
return;
|
|
463
|
}
|
|
464
|
|
|
465
|
/**
|
|
466
|
* @param elLabel
|
|
467
|
* @return
|
|
468
|
*/
|
|
469
|
private Language getLanguage(Element elLanguage) {
|
|
470
|
String lang = elLanguage.getAttributeValue("lang",xmlNamespace);
|
|
471
|
Language language = null;
|
|
472
|
if (StringUtils.isNotBlank(lang)) {
|
|
473
|
language = getTermService().getLanguageByIso(lang.substring(0, 2));
|
|
474
|
} else {
|
|
475
|
language = datasetLanguage;
|
|
476
|
}
|
|
477
|
return language;
|
|
478
|
}
|
|
479
|
|
|
480
|
|
|
481
|
// imports the representation (label, detail, lang) of a particular SDD element
|
|
482
|
protected void importTechnicalMetadata(Element root, Namespace sddNamespace, SDDImportConfigurator sddConfig){
|
|
483
|
Element elTechnicalMetadata = root.getChild("TechnicalMetadata", sddNamespace);
|
|
484
|
String nameCreated = elTechnicalMetadata.getAttributeValue("created");
|
|
485
|
sourceReference = sddConfig.getSourceReference();
|
|
486
|
|
|
487
|
if (nameCreated != null) {
|
|
488
|
if (!nameCreated.equals("")) {
|
|
489
|
int year = Integer.parseInt(nameCreated.substring(0,4));
|
|
490
|
int monthOfYear = Integer.parseInt(nameCreated.substring(5,7));
|
|
491
|
int dayOfMonth = Integer.parseInt(nameCreated.substring(8,10));
|
|
492
|
int hourOfDay = Integer.parseInt(nameCreated.substring(11,13));
|
|
493
|
int minuteOfHour = Integer.parseInt(nameCreated.substring(14,16));
|
|
494
|
int secondOfMinute = Integer.parseInt(nameCreated.substring(17,19));
|
|
495
|
DateTime created = new DateTime(year,monthOfYear,dayOfMonth,hourOfDay,minuteOfHour,secondOfMinute,0);
|
|
496
|
sourceReference.setCreated(created);
|
|
497
|
sec.setCreated(created);
|
|
498
|
}
|
|
499
|
}
|
|
500
|
|
|
501
|
// <Generator name="n/a, handcrafted instance document" version="n/a"/>
|
|
502
|
Element elGenerator = elTechnicalMetadata.getChild("Generator", sddNamespace);
|
|
503
|
generatorName = elGenerator.getAttributeValue("name");
|
|
504
|
generatorVersion = elGenerator.getAttributeValue("version");
|
|
505
|
|
|
506
|
sec.addAnnotation(Annotation.NewDefaultLanguageInstance(generatorName + " - " + generatorVersion));
|
|
507
|
sourceReference.addAnnotation(Annotation.NewDefaultLanguageInstance(generatorName + " - " + generatorVersion));
|
|
508
|
|
|
509
|
}
|
|
510
|
|
|
511
|
// imports the complete dataset information
|
|
512
|
protected boolean importDataset(Element elDataset, Namespace sddNamespace, SDDImportState state){ // <Dataset xml:lang="en-us">
|
|
513
|
boolean success = true;
|
|
514
|
SDDImportConfigurator sddConfig = state.getConfig();
|
|
515
|
importDatasetLanguage(elDataset,sddConfig);
|
|
516
|
importDatasetRepresentation(elDataset, sddNamespace);
|
|
517
|
importRevisionData(elDataset, sddNamespace);
|
|
518
|
importIPRStatements(elDataset, sddNamespace, sddConfig);
|
|
519
|
importTaxonNames(elDataset, sddNamespace, sddConfig);
|
|
520
|
importDescriptiveConcepts(elDataset, sddNamespace, sddConfig);
|
|
521
|
success &= importCharacters(elDataset, sddNamespace, sddConfig);
|
|
522
|
importCharacterTrees(elDataset, sddNamespace, sddConfig, success);
|
|
523
|
|
|
524
|
MarkerType editorMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerEditor, "editor", "Editor", "edt");
|
|
525
|
MarkerType geographicAreaMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerSDDGeographicArea, "SDDGeographicArea", "SDDGeographicArea", "ga");
|
|
526
|
MarkerType descriptiveConceptMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerDescriptiveConcept, "DescriptiveConcept", "Descriptive Concept", "DC");
|
|
527
|
markerTypes.add(editorMarkerType);
|
|
528
|
markerTypes.add(geographicAreaMarkerType);
|
|
529
|
markerTypes.add(descriptiveConceptMarkerType);
|
|
530
|
|
|
531
|
//saving of all imported data into the CDM db
|
|
532
|
saveFeatures();
|
|
533
|
saveModifiers();
|
|
534
|
saveStates();
|
|
535
|
saveMarkerType();
|
|
536
|
saveAreas(geographicAreaMarkerType);
|
|
537
|
saveUnits();
|
|
538
|
saveStatisticalMeasure();
|
|
539
|
saveAnnotationType();
|
|
540
|
|
|
541
|
success &= importCodedDescriptions(elDataset, sddNamespace, sddConfig);
|
|
542
|
importAgents(elDataset, sddNamespace, sddConfig, success);
|
|
543
|
importPublications(elDataset, sddNamespace, sddConfig, success);
|
|
544
|
importMediaObjects(elDataset, sddNamespace, sddConfig, success);
|
|
545
|
importTaxonHierarchies(elDataset, sddNamespace, sddConfig, success);
|
|
546
|
importGeographicAreas(elDataset, sddNamespace, sddConfig);
|
|
547
|
importSpecimens(elDataset,sddNamespace, sddConfig);
|
|
548
|
|
|
549
|
|
|
550
|
|
|
551
|
if ((authors != null)||(editors != null)) {
|
|
552
|
Team team = Team.NewInstance();
|
|
553
|
if (authors != null) {
|
|
554
|
for (Person author : authors.values()){
|
|
555
|
team.addTeamMember(author);
|
|
556
|
}
|
|
557
|
}
|
|
558
|
if (editors != null) {
|
|
559
|
Marker marker = Marker.NewInstance();
|
|
560
|
marker.setMarkerType(editorMarkerType);
|
|
561
|
for (Person editor : editors.values()){
|
|
562
|
Person edit = editor;
|
|
563
|
edit.addMarker(marker);
|
|
564
|
team.addTeamMember(edit);
|
|
565
|
}
|
|
566
|
}
|
|
567
|
sec.setAuthorTeam(team);
|
|
568
|
sourceReference.setAuthorTeam(team);
|
|
569
|
}
|
|
570
|
|
|
571
|
if (copyright != null) {
|
|
572
|
sourceReference.addRights(copyright);
|
|
573
|
sec.addRights(copyright);
|
|
574
|
}
|
|
575
|
|
|
576
|
// Returns a CdmApplicationController created by the values of this configuration.
|
|
577
|
IDescriptionService descriptionService = getDescriptionService();
|
|
578
|
|
|
579
|
for (TaxonDescription taxonDescription : taxonDescriptions.values()){
|
|
580
|
// Persists a Description
|
|
581
|
descriptionService.save(taxonDescription);
|
|
582
|
}
|
|
583
|
|
|
584
|
for (String ref : taxonDescriptions.keySet()){
|
|
585
|
TaxonDescription td = taxonDescriptions.get(ref);
|
|
586
|
if (citations.containsKey(ref)) {
|
|
587
|
ReferenceBase publication = publications.get(citations.get(ref));
|
|
588
|
if (locations.containsKey(ref)) {
|
|
589
|
Annotation location = Annotation.NewInstance(locations.get(ref), datasetLanguage);
|
|
590
|
AnnotationType annotationType = AnnotationType.NewInstance("", "location", "");
|
|
591
|
annotationTypes.add(annotationType);
|
|
592
|
location.setAnnotationType(annotationType);
|
|
593
|
(publication).addAnnotation(location);
|
|
594
|
}
|
|
595
|
td.addDescriptionSource(publication);
|
|
596
|
}
|
|
597
|
}
|
|
598
|
logger.info("end makeTaxonDescriptions ...");
|
|
599
|
|
|
600
|
|
|
601
|
// for (Iterator<TermVocabulary<Modifier>> k = termVocabularyStates.iterator() ; k.hasNext() ;){
|
|
602
|
// TermVocabulary<Modifier> termVocabulary = k.next();
|
|
603
|
// getVocabularyService().save(termVocabulary); //XIM
|
|
604
|
// }
|
|
605
|
|
|
606
|
|
|
607
|
//sddConfig.setSourceReference(sourceReference);
|
|
608
|
|
|
609
|
|
|
610
|
if (descriptiveConcepts != null) {
|
|
611
|
for (Feature feature : descriptiveConcepts) {
|
|
612
|
Marker marker = Marker.NewInstance();
|
|
613
|
marker.setMarkerType(descriptiveConceptMarkerType);
|
|
614
|
feature.addMarker(marker);
|
|
615
|
}
|
|
616
|
}
|
|
617
|
saveFeatures();
|
|
618
|
|
|
619
|
/*Marker markerd = Marker.NewInstance();
|
|
620
|
markerd.setMarkerType(descriptiveConceptMarker);
|
|
621
|
Feature fiture = Feature.NewInstance("Fitoure","Fitoure","Fitoure");
|
|
622
|
fiture.addMarker(markerd);
|
|
623
|
TermVocabulary<Modifier> termVocabularyState = new TermVocabulary<Modifier>("test","test","test","test");
|
|
624
|
Modifier modif = new Modifier("zoub","zab","zib");
|
|
625
|
termVocabularyState.addTerm(modif);
|
|
626
|
getVocabularyService().save(termVocabularyState);
|
|
627
|
fiture.addRecommendedModifierEnumeration(termVocabularyState);
|
|
628
|
termService.save(modif);
|
|
629
|
termService.save(fiture);*/
|
|
630
|
|
|
631
|
//XIMtermService.save(editorMarkerType);
|
|
632
|
|
|
633
|
//XIMtermService.save(geographicAreaMarkerType);
|
|
634
|
|
|
635
|
// referenceService.saveReference(sourceReference);
|
|
636
|
for (ReferenceBase publication : publications.values()){
|
|
637
|
getReferenceService().save(publication);
|
|
638
|
}
|
|
639
|
|
|
640
|
for (FeatureTree featureTree : featureTrees) {
|
|
641
|
getFeatureTreeService().save(featureTree);
|
|
642
|
}
|
|
643
|
for (TaxonomicTree taxonomicTree : taxonomicTrees) {
|
|
644
|
getTaxonTreeService().save(taxonomicTree);
|
|
645
|
}
|
|
646
|
for (Specimen specimen : specimens.values()) {
|
|
647
|
getOccurrenceService().save(specimen);
|
|
648
|
}
|
|
649
|
logger.info("end of persistence ...");
|
|
650
|
|
|
651
|
return success;
|
|
652
|
}
|
|
653
|
|
|
654
|
private void saveAnnotationType() {
|
|
655
|
for (AnnotationType annotationType: annotationTypes){
|
|
656
|
getTermService().save(annotationType);
|
|
657
|
}
|
|
658
|
}
|
|
659
|
|
|
660
|
private void saveStatisticalMeasure() {
|
|
661
|
for (StatisticalMeasure sm : statisticalMeasures){
|
|
662
|
getTermService().save(sm);
|
|
663
|
}
|
|
664
|
}
|
|
665
|
|
|
666
|
private void saveUnits() {
|
|
667
|
if (units != null) {
|
|
668
|
for (MeasurementUnit unit : units.values()){
|
|
669
|
if (unit != null) {
|
|
670
|
getTermService().save(unit);
|
|
671
|
}
|
|
672
|
}
|
|
673
|
}
|
|
674
|
}
|
|
675
|
|
|
676
|
private void saveAreas(MarkerType geographicAreaMarkerType) {
|
|
677
|
for (NamedArea area : namedAreas.values() ){
|
|
678
|
Marker marker = Marker.NewInstance();
|
|
679
|
marker.setMarkerType(geographicAreaMarkerType);
|
|
680
|
area.addMarker(marker);
|
|
681
|
getTermService().save(area);
|
|
682
|
}
|
|
683
|
}
|
|
684
|
|
|
685
|
private void saveStates() {
|
|
686
|
for (State state : states.values() ){
|
|
687
|
getTermService().save(state);
|
|
688
|
}
|
|
689
|
}
|
|
690
|
|
|
691
|
private void saveMarkerType() {
|
|
692
|
for (MarkerType markerType : markerTypes){
|
|
693
|
getTermService().save(markerType);
|
|
694
|
}
|
|
695
|
}
|
|
696
|
|
|
697
|
private void saveModifiers() {
|
|
698
|
for (Modifier modifier : modifiers.values() ){
|
|
699
|
getTermService().save(modifier);
|
|
700
|
}
|
|
701
|
}
|
|
702
|
|
|
703
|
private void saveFeatures() {
|
|
704
|
for (Feature feature : features.values() ){
|
|
705
|
getTermService().save(feature);
|
|
706
|
}
|
|
707
|
}
|
|
708
|
|
|
709
|
// imports the default language of the dataset
|
|
710
|
protected void importDatasetLanguage(Element elDataset, SDDImportConfigurator sddConfig){
|
|
711
|
String nameLang = elDataset.getAttributeValue("lang",xmlNamespace);
|
|
712
|
|
|
713
|
if (!nameLang.equals("")) {
|
|
714
|
String iso = nameLang.substring(0, 2);
|
|
715
|
datasetLanguage = getTermService().getLanguageByIso(iso);
|
|
716
|
} else {
|
|
717
|
datasetLanguage = Language.DEFAULT();
|
|
718
|
}
|
|
719
|
if (datasetLanguage == null) {
|
|
720
|
datasetLanguage = Language.DEFAULT();
|
|
721
|
}
|
|
722
|
}
|
|
723
|
|
|
724
|
// imports the specimens
|
|
725
|
protected void importSpecimens(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig) {
|
|
726
|
logger.info("start Specimens ...");
|
|
727
|
/* <Specimens>
|
|
728
|
<Specimen id="sp1">
|
|
729
|
<Representation>
|
|
730
|
<Label>TJM45337</Label>
|
|
731
|
</Representation>
|
|
732
|
</Specimen>
|
|
733
|
</Specimens>
|
|
734
|
*/
|
|
735
|
Element elSpecimens = elDataset.getChild("Specimens",sddNamespace);
|
|
736
|
if (elSpecimens != null){
|
|
737
|
List<Element> listSpecimens = elSpecimens.getChildren("Specimen", sddNamespace);
|
|
738
|
int j = 0;
|
|
739
|
for (Element elSpecimen : listSpecimens) {
|
|
740
|
String id = elSpecimen.getAttributeValue("id");
|
|
741
|
Specimen specimen = null;
|
|
742
|
if (!id.equals("")) {
|
|
743
|
specimen = Specimen.NewInstance();
|
|
744
|
specimens.put(id,specimen);
|
|
745
|
importRepresentation(elSpecimen, sddNamespace, specimen, id, sddConfig);
|
|
746
|
}
|
|
747
|
}
|
|
748
|
|
|
749
|
}
|
|
750
|
}
|
|
751
|
|
|
752
|
// imports the revision data associated with the Dataset (authors, modifications)
|
|
753
|
protected void importRevisionData(Element elDataset, Namespace sddNamespace){
|
|
754
|
// <RevisionData>
|
|
755
|
logger.info("start RevisionData ...");
|
|
756
|
Element elRevisionData = elDataset.getChild("RevisionData",sddNamespace);
|
|
757
|
if (elRevisionData != null){
|
|
758
|
// <Creators>
|
|
759
|
Element elCreators = elRevisionData.getChild("Creators",sddNamespace);
|
|
760
|
|
|
761
|
// <Agent role="aut" ref="a1"/>
|
|
762
|
List<Element> listAgents = elCreators.getChildren("Agent", sddNamespace);
|
|
763
|
|
|
764
|
int j = 0;
|
|
765
|
//for each Agent
|
|
766
|
for (Element elAgent : listAgents){
|
|
767
|
|
|
768
|
String role = elAgent.getAttributeValue("role");
|
|
769
|
String ref = elAgent.getAttributeValue("ref");
|
|
770
|
if (role.equals("aut")) {
|
|
771
|
if(!ref.equals("")) {
|
|
772
|
authors.put(ref, null);
|
|
773
|
}
|
|
774
|
}
|
|
775
|
if (role.equals("edt")) {
|
|
776
|
if(!ref.equals("")) {
|
|
777
|
editors.put(ref, null);
|
|
778
|
}
|
|
779
|
}
|
|
780
|
if ((++j % modCount) == 0){ logger.info("Agents handled: " + j);}
|
|
781
|
|
|
782
|
}
|
|
783
|
|
|
784
|
// <DateModified>2006-04-08T00:00:00</DateModified>
|
|
785
|
String stringDateModified = (String)ImportHelper.getXmlInputValue(elRevisionData, "DateModified",sddNamespace);
|
|
786
|
|
|
787
|
if (stringDateModified != null) {
|
|
788
|
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss");
|
|
789
|
Date d = null;
|
|
790
|
try {
|
|
791
|
d = sdf.parse(stringDateModified);
|
|
792
|
} catch(Exception e) {
|
|
793
|
System.err.println("Exception :");
|
|
794
|
e.printStackTrace();
|
|
795
|
}
|
|
796
|
|
|
797
|
DateTime updated = null;
|
|
798
|
if (d != null) {
|
|
799
|
updated = new DateTime(d);
|
|
800
|
sourceReference.setUpdated(updated);
|
|
801
|
sec.setUpdated(updated);
|
|
802
|
}
|
|
803
|
}
|
|
804
|
}
|
|
805
|
}
|
|
806
|
|
|
807
|
// imports ipr statements associated with a dataset
|
|
808
|
protected void importIPRStatements(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
|
|
809
|
// <IPRStatements>
|
|
810
|
logger.info("start IPRStatements ...");
|
|
811
|
Element elIPRStatements = elDataset.getChild("IPRStatements",sddNamespace);
|
|
812
|
// <IPRStatement role="Copyright">
|
|
813
|
if (elIPRStatements != null) {
|
|
814
|
List<Element> listIPRStatements = elIPRStatements.getChildren("IPRStatement", sddNamespace);
|
|
815
|
int j = 0;
|
|
816
|
//for each IPRStatement
|
|
817
|
|
|
818
|
for (Element elIPRStatement : listIPRStatements){
|
|
819
|
|
|
820
|
String role = elIPRStatement.getAttributeValue("role");
|
|
821
|
// <Label xml:lang="en-au">(c) 2003-2006 Centre for Occasional Botany.</Label>
|
|
822
|
Element elLabel = elIPRStatement.getChild("Label",sddNamespace);
|
|
823
|
String lang = "";
|
|
824
|
if (elLabel != null) {
|
|
825
|
lang = elLabel.getAttributeValue("lang",xmlNamespace);
|
|
826
|
}
|
|
827
|
String label = (String)ImportHelper.getXmlInputValue(elIPRStatement, "Label",sddNamespace);
|
|
828
|
|
|
829
|
if (role.equals("Copyright")) {
|
|
830
|
Language iprLanguage = null;
|
|
831
|
if (lang != null) {
|
|
832
|
if (!lang.equals("")) {
|
|
833
|
iprLanguage = getTermService().getLanguageByIso(lang.substring(0, 2));
|
|
834
|
} else {
|
|
835
|
iprLanguage = datasetLanguage;
|
|
836
|
}
|
|
837
|
}
|
|
838
|
if (iprLanguage == null) {
|
|
839
|
iprLanguage = datasetLanguage;
|
|
840
|
}
|
|
841
|
copyright = Rights.NewInstance(label, iprLanguage);
|
|
842
|
}
|
|
843
|
|
|
844
|
if (copyright != null) {
|
|
845
|
sourceReference.addRights(copyright);
|
|
846
|
sec.addRights(copyright);
|
|
847
|
}
|
|
848
|
|
|
849
|
if ((++j % modCount) == 0){ logger.info("IPRStatements handled: " + j);}
|
|
850
|
|
|
851
|
}
|
|
852
|
}
|
|
853
|
}
|
|
854
|
|
|
855
|
// imports the taxon names
|
|
856
|
protected void importTaxonNames(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
|
|
857
|
// <TaxonNames>
|
|
858
|
logger.info("start TaxonNames ...");
|
|
859
|
Element elTaxonNames = elDataset.getChild("TaxonNames",sddNamespace);
|
|
860
|
// <TaxonName id="t1" uri="urn:lsid:authority:namespace:my-own-id">
|
|
861
|
if (elTaxonNames != null) {
|
|
862
|
List<Element> listTaxonNames = elTaxonNames.getChildren("TaxonName", sddNamespace);
|
|
863
|
int j = 0;
|
|
864
|
//for each TaxonName
|
|
865
|
for (Element elTaxonName : listTaxonNames){
|
|
866
|
|
|
867
|
String id = elTaxonName.getAttributeValue("id");
|
|
868
|
String uri = elTaxonName.getAttributeValue("uri");
|
|
869
|
|
|
870
|
NonViralName tnb = null;
|
|
871
|
if (!id.equals("")) {
|
|
872
|
tnb = NonViralName.NewInstance(null);
|
|
873
|
IdentifiableSource source = null;
|
|
874
|
if (uri != null) {
|
|
875
|
if (!uri.equals("")) {
|
|
876
|
source = IdentifiableSource.NewInstance(id, "TaxonName", ReferenceFactory.newGeneric(), uri);
|
|
877
|
}
|
|
878
|
} else {
|
|
879
|
source = IdentifiableSource.NewInstance(id, "TaxonName");
|
|
880
|
}
|
|
881
|
tnb.addSource(source);
|
|
882
|
taxonNameBases.put(id,tnb);
|
|
883
|
}
|
|
884
|
|
|
885
|
// <Representation>
|
|
886
|
// <Label xml:lang="la">Viola hederacea Labill.</Label>
|
|
887
|
importRepresentation(elTaxonName, sddNamespace, tnb, id, sddConfig);
|
|
888
|
|
|
889
|
if ((++j % modCount) == 0){ logger.info("TaxonNames handled: " + j);}
|
|
890
|
|
|
891
|
}
|
|
892
|
}
|
|
893
|
}
|
|
894
|
|
|
895
|
// imports the characters (categorical, quantitative and text ; sequence characters not supported) which correspond to CDM Features
|
|
896
|
protected boolean importCharacters(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
|
|
897
|
boolean success = true;
|
|
898
|
// <Characters>
|
|
899
|
logger.info("start Characters ...");
|
|
900
|
Element elCharacters = elDataset.getChild("Characters", sddNamespace);
|
|
901
|
|
|
902
|
// <CategoricalCharacter id="c1">
|
|
903
|
if (elCharacters != null) {
|
|
904
|
success &= handleCategoricalData(sddNamespace, sddConfig, elCharacters);
|
|
905
|
success &= handleQuantitativeData(sddNamespace, sddConfig, elCharacters);
|
|
906
|
success &= handleTextCharacters(sddNamespace, sddConfig, elCharacters);
|
|
907
|
}
|
|
908
|
|
|
909
|
/*for (Iterator<Feature> f = features.values().iterator() ; f.hasNext() ;){
|
|
910
|
featureSet.add(f.next()); //XIM Why this line ?
|
|
911
|
}*/
|
|
912
|
|
|
913
|
return success;
|
|
914
|
|
|
915
|
}
|
|
916
|
|
|
917
|
/**
|
|
918
|
* @param sddNamespace
|
|
919
|
* @param sddConfig
|
|
920
|
* @param success
|
|
921
|
* @param elCharacters
|
|
922
|
* @return
|
|
923
|
*/
|
|
924
|
private boolean handleCategoricalData(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCharacters) {
|
|
925
|
boolean success = true;
|
|
926
|
List<Element> elCategoricalCharacters = elCharacters.getChildren("CategoricalCharacter", sddNamespace);
|
|
927
|
int j = 0;
|
|
928
|
for (Element elCategoricalCharacter : elCategoricalCharacters){
|
|
929
|
try {
|
|
930
|
|
|
931
|
String idCC = elCategoricalCharacter.getAttributeValue("id");
|
|
932
|
Feature categoricalCharacter = Feature.NewInstance();
|
|
933
|
categoricalCharacter.setKindOf(Feature.DESCRIPTION());
|
|
934
|
importRepresentation(elCategoricalCharacter, sddNamespace, categoricalCharacter, idCC, sddConfig);
|
|
935
|
categoricalCharacter.setSupportsCategoricalData(true);
|
|
936
|
|
|
937
|
// <States>
|
|
938
|
Element elStates = elCategoricalCharacter.getChild("States",sddNamespace);
|
|
939
|
|
|
940
|
// <StateDefinition id="s1">
|
|
941
|
List<Element> elStateDefinitions = elStates.getChildren("StateDefinition",sddNamespace);
|
|
942
|
TermVocabulary<State> termVocabularyState = new TermVocabulary<State>();
|
|
943
|
int k = 0;
|
|
944
|
//for each StateDefinition
|
|
945
|
for (Element elStateDefinition : elStateDefinitions){
|
|
946
|
|
|
947
|
if ((++k % modCount) == 0){ logger.info("StateDefinitions handled: " + (k-1));}
|
|
948
|
|
|
949
|
String idS = elStateDefinition.getAttributeValue("id");
|
|
950
|
State state = states.get(idS);
|
|
951
|
if (state == null){
|
|
952
|
state = State.NewInstance();
|
|
953
|
}else{
|
|
954
|
logger.debug("State duplicate found");
|
|
955
|
}
|
|
956
|
importRepresentation(elStateDefinition, sddNamespace, state, idS, sddConfig);
|
|
957
|
|
|
958
|
//StateData stateData = StateData.NewInstance();
|
|
959
|
//stateData.setState(state);
|
|
960
|
termVocabularyState.addTerm(state);
|
|
961
|
states.put(idS,state);
|
|
962
|
}
|
|
963
|
categoricalCharacter.addSupportedCategoricalEnumeration(termVocabularyState);
|
|
964
|
features.put(idCC, categoricalCharacter);
|
|
965
|
|
|
966
|
} catch (Exception e) {
|
|
967
|
logger.warn("Import of CategoricalCharacter " + j + " failed.");
|
|
968
|
success = false;
|
|
969
|
}
|
|
970
|
|
|
971
|
if ((++j % modCount) == 0){ logger.info("CategoricalCharacters handled: " + j);}
|
|
972
|
|
|
973
|
}
|
|
974
|
return success;
|
|
975
|
}
|
|
976
|
|
|
977
|
/**
|
|
978
|
* @param sddNamespace
|
|
979
|
* @param sddConfig
|
|
980
|
* @param elCharacters
|
|
981
|
*/
|
|
982
|
private boolean handleQuantitativeData(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCharacters) {
|
|
983
|
boolean success = true;
|
|
984
|
int j;
|
|
985
|
// <QuantitativeCharacter id="c2">
|
|
986
|
List<Element> elQuantitativeCharacters = elCharacters.getChildren("QuantitativeCharacter", sddNamespace);
|
|
987
|
j = 0;
|
|
988
|
//for each QuantitativeCharacter
|
|
989
|
for (Element elQuantitativeCharacter : elQuantitativeCharacters){
|
|
990
|
|
|
991
|
try {
|
|
992
|
|
|
993
|
String idQC = elQuantitativeCharacter.getAttributeValue("id");
|
|
994
|
|
|
995
|
// <Representation>
|
|
996
|
// <Label>Leaf length</Label>
|
|
997
|
// </Representation>
|
|
998
|
Feature quantitativeCharacter = Feature.NewInstance();
|
|
999
|
quantitativeCharacter.setKindOf(Feature.DESCRIPTION());
|
|
1000
|
importRepresentation(elQuantitativeCharacter, sddNamespace, quantitativeCharacter, idQC, sddConfig);
|
|
1001
|
|
|
1002
|
quantitativeCharacter.setSupportsQuantitativeData(true);
|
|
1003
|
|
|
1004
|
// <MeasurementUnit>
|
|
1005
|
// <Label role="Abbrev">m</Label>
|
|
1006
|
// </MeasurementUnit>
|
|
1007
|
Element elMeasurementUnit = elQuantitativeCharacter.getChild("MeasurementUnit",sddNamespace);
|
|
1008
|
String label = "";
|
|
1009
|
String role = "";
|
|
1010
|
if (elMeasurementUnit != null) {
|
|
1011
|
Element elLabel = elMeasurementUnit.getChild("Label",sddNamespace);
|
|
1012
|
role = elLabel.getAttributeValue("role");
|
|
1013
|
label = (String)ImportHelper.getXmlInputValue(elMeasurementUnit, "Label",sddNamespace);
|
|
1014
|
}
|
|
1015
|
|
|
1016
|
MeasurementUnit unit = null;
|
|
1017
|
if (!label.equals("")){
|
|
1018
|
if (role != null) {
|
|
1019
|
if (role.equals("Abbrev")){
|
|
1020
|
unit = MeasurementUnit.NewInstance(label,label,label);
|
|
1021
|
}
|
|
1022
|
} else {
|
|
1023
|
unit = MeasurementUnit.NewInstance(label,label,label);
|
|
1024
|
}
|
|
1025
|
}
|
|
1026
|
|
|
1027
|
if (unit != null) {
|
|
1028
|
units.put(idQC, unit);
|
|
1029
|
}
|
|
1030
|
|
|
1031
|
//<Default>
|
|
1032
|
// <MeasurementUnitPrefix>milli</MeasurementUnitPrefix>
|
|
1033
|
//</Default>
|
|
1034
|
Element elDefault = elQuantitativeCharacter.getChild("Default",sddNamespace);
|
|
1035
|
if (elDefault != null) {
|
|
1036
|
String measurementUnitPrefix = (String)ImportHelper.getXmlInputValue(elDefault, "MeasurementUnitPrefix",sddNamespace);
|
|
1037
|
if (! measurementUnitPrefix.equals("")){
|
|
1038
|
defaultUnitPrefixes.put(idQC, measurementUnitPrefix);
|
|
1039
|
}
|
|
1040
|
}
|
|
1041
|
|
|
1042
|
features.put(idQC, quantitativeCharacter);
|
|
1043
|
|
|
1044
|
} catch (Exception e) {
|
|
1045
|
//FIXME
|
|
1046
|
logger.warn("Import of QuantitativeCharacter " + j + " failed.");
|
|
1047
|
success = false;
|
|
1048
|
}
|
|
1049
|
|
|
1050
|
if ((++j % modCount) == 0){ logger.info("QuantitativeCharacters handled: " + j);}
|
|
1051
|
|
|
1052
|
}
|
|
1053
|
return success;
|
|
1054
|
}
|
|
1055
|
|
|
1056
|
private boolean handleTextCharacters(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCharacters) {
|
|
1057
|
boolean success = true;
|
|
1058
|
int j;
|
|
1059
|
// <TextCharacter id="c3">
|
|
1060
|
List<Element> elTextCharacters = elCharacters.getChildren("TextCharacter", sddNamespace);
|
|
1061
|
j = 0;
|
|
1062
|
//for each TextCharacter
|
|
1063
|
for (Element elTextCharacter : elTextCharacters){
|
|
1064
|
|
|
1065
|
try {
|
|
1066
|
|
|
1067
|
String idTC = elTextCharacter.getAttributeValue("id");
|
|
1068
|
|
|
1069
|
// <Representation>
|
|
1070
|
// <Label xml:lang="en">Leaf features not covered by other characters</Label>
|
|
1071
|
// </Representation>
|
|
1072
|
Feature textCharacter = Feature.NewInstance();
|
|
1073
|
textCharacter.setKindOf(Feature.DESCRIPTION());
|
|
1074
|
importRepresentation(elTextCharacter, sddNamespace, textCharacter, idTC, sddConfig);
|
|
1075
|
|
|
1076
|
textCharacter.setSupportsTextData(true);
|
|
1077
|
|
|
1078
|
features.put(idTC, textCharacter);
|
|
1079
|
|
|
1080
|
} catch (Exception e) {
|
|
1081
|
//FIXME
|
|
1082
|
logger.warn("Import of TextCharacter " + j + " failed.");
|
|
1083
|
success = false;
|
|
1084
|
}
|
|
1085
|
|
|
1086
|
if ((++j % modCount) == 0){ logger.info("TextCharacters handled: " + j);}
|
|
1087
|
|
|
1088
|
}
|
|
1089
|
return success;
|
|
1090
|
}
|
|
1091
|
|
|
1092
|
// imports the descriptions of taxa
|
|
1093
|
protected boolean importCodedDescriptions(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
|
|
1094
|
boolean success = true;
|
|
1095
|
|
|
1096
|
// <CodedDescriptions>
|
|
1097
|
logger.info("start CodedDescriptions ...");
|
|
1098
|
Element elCodedDescriptions = elDataset.getChild("CodedDescriptions",sddNamespace);
|
|
1099
|
|
|
1100
|
// <CodedDescription id="D101">
|
|
1101
|
if (elCodedDescriptions != null) {
|
|
1102
|
List<Element> listCodedDescriptions = elCodedDescriptions.getChildren("CodedDescription", sddNamespace);
|
|
1103
|
int j = 0;
|
|
1104
|
//for each CodedDescription
|
|
1105
|
for (Element elCodedDescription : listCodedDescriptions){
|
|
1106
|
success &= handleCodedDescription(sddNamespace, sddConfig, elCodedDescription, j);
|
|
1107
|
if ((++j % modCount) == 0){ logger.info("CodedDescriptions handled: " + j);}
|
|
1108
|
}
|
|
1109
|
}
|
|
1110
|
return success;
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
/**
|
|
1114
|
* @param sddNamespace
|
|
1115
|
* @param sddConfig
|
|
1116
|
* @param j
|
|
1117
|
* @param elCodedDescription
|
|
1118
|
* @return
|
|
1119
|
*/
|
|
1120
|
private boolean handleCodedDescription(Namespace sddNamespace, SDDImportConfigurator sddConfig, Element elCodedDescription, int j) {
|
|
1121
|
boolean success = true ;
|
|
1122
|
try {
|
|
1123
|
|
|
1124
|
String idCD = elCodedDescription.getAttributeValue("id");
|
|
1125
|
|
|
1126
|
// <Representation>
|
|
1127
|
// <Label><i>Viola hederacea</i> Labill. as revised by R. Morris April 8, 2006</Label>
|
|
1128
|
// </Representation>
|
|
1129
|
TaxonDescription taxonDescription = TaxonDescription.NewInstance();
|
|
1130
|
importRepresentation(elCodedDescription, sddNamespace, taxonDescription, idCD, sddConfig);
|
|
1131
|
|
|
1132
|
// <Scope>
|
|
1133
|
// <TaxonName ref="t1"/>
|
|
1134
|
// <Citation ref="p1" location="p. 30"/>
|
|
1135
|
// </Scope>
|
|
1136
|
Element elScope = elCodedDescription.getChild("Scope", sddNamespace);
|
|
1137
|
Taxon taxon;
|
|
1138
|
if (elScope != null) {
|
|
1139
|
taxon = handleCDScope(sddNamespace, sddConfig, idCD, elScope);
|
|
1140
|
} else {//in case no taxon is linked to the description, a new one is created
|
|
1141
|
taxon = handleCDNoScope(sddNamespace, sddConfig, elCodedDescription);
|
|
1142
|
}
|
|
1143
|
|
|
1144
|
// <SummaryData>
|
|
1145
|
Element elSummaryData = elCodedDescription.getChild("SummaryData",sddNamespace);
|
|
1146
|
if (elSummaryData != null) {
|
|
1147
|
handleSummaryCategoricalData(sddNamespace, taxonDescription, elSummaryData);
|
|
1148
|
handleSummaryQuantitativeData(sddNamespace, taxonDescription, elSummaryData);
|
|
1149
|
handleSummaryTextData(sddNamespace, taxonDescription, elSummaryData);
|
|
1150
|
}
|
|
1151
|
|
|
1152
|
if (taxon != null) {
|
|
1153
|
taxon.addDescription(taxonDescription);
|
|
1154
|
}
|
|
1155
|
|
|
1156
|
taxonDescription.setDescriptiveSystem(featureSet);
|
|
1157
|
|
|
1158
|
taxonDescriptions.put(idCD, taxonDescription);//FIXME
|
|
1159
|
|
|
1160
|
} catch (Exception e) {
|
|
1161
|
//FIXME
|
|
1162
|
logger.warn("Import of CodedDescription " + j + " failed.", e);
|
|
1163
|
success = false;
|
|
1164
|
}
|
|
1165
|
return success;
|
|
1166
|
}
|
|
1167
|
|
|
1168
|
/**
|
|
1169
|
* @param sddNamespace
|
|
1170
|
* @param sddConfig
|
|
1171
|
* @param elCodedDescription
|
|
1172
|
* @param taxon
|
|
1173
|
* @return
|
|
1174
|
*/
|
|
1175
|
private Taxon handleCDNoScope(Namespace sddNamespace,
|
|
1176
|
SDDImportConfigurator sddConfig, Element elCodedDescription ) {
|
|
1177
|
Taxon taxon = null;
|
|
1178
|
NonViralName nonViralName = NonViralName.NewInstance(null);
|
|
1179
|
String id = new String("" + taxonNamesCount);
|
|
1180
|
IdentifiableSource source = IdentifiableSource.NewInstance(id, "TaxonName");
|
|
1181
|
importRepresentation(elCodedDescription, sddNamespace, nonViralName, id, sddConfig);
|
|
1182
|
|
|
1183
|
if(sddConfig.isDoMatchTaxa()){
|
|
1184
|
taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache());
|
|
1185
|
}
|
|
1186
|
|
|
1187
|
if(taxon != null){
|
|
1188
|
nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
|
|
1189
|
// taxonNameBases.put(id ,tnb);
|
|
1190
|
// taxonNamesCount++;
|
|
1191
|
logger.info("using existing Taxon" + taxon.getTitleCache());
|
|
1192
|
} else {
|
|
1193
|
nonViralName.addSource(source);
|
|
1194
|
taxonNameBases.put(id ,nonViralName);
|
|
1195
|
taxonNamesCount++;
|
|
1196
|
logger.info("creating new Taxon from TaxonName" + nonViralName.getTitleCache());
|
|
1197
|
taxon = Taxon.NewInstance(nonViralName, sec);
|
|
1198
|
}
|
|
1199
|
return taxon;
|
|
1200
|
}
|
|
1201
|
|
|
1202
|
/**
|
|
1203
|
* @param sddNamespace
|
|
1204
|
* @param sddConfig
|
|
1205
|
* @param idCD
|
|
1206
|
* @param elScope
|
|
1207
|
* @param taxon
|
|
1208
|
* @return
|
|
1209
|
*/
|
|
1210
|
private Taxon handleCDScope(Namespace sddNamespace, SDDImportConfigurator sddConfig,
|
|
1211
|
String idCD, Element elScope) {
|
|
1212
|
Taxon taxon = null;
|
|
1213
|
Element elTaxonName = elScope.getChild("TaxonName", sddNamespace);
|
|
1214
|
String ref = elTaxonName.getAttributeValue("ref");
|
|
1215
|
NonViralName nonViralName = taxonNameBases.get(ref);
|
|
1216
|
|
|
1217
|
if(sddConfig.isDoMatchTaxa()){
|
|
1218
|
taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache());
|
|
1219
|
}
|
|
1220
|
|
|
1221
|
if(taxon != null){
|
|
1222
|
logger.info("using existing Taxon" + taxon.getTitleCache());
|
|
1223
|
if(!nonViralName.getUuid().equals(taxon.getName().getUuid())){
|
|
1224
|
logger.warn("TaxonNameBase entity of existing taxon does not match Name in list -> replacing Name in list");
|
|
1225
|
nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
|
|
1226
|
}
|
|
1227
|
} else {
|
|
1228
|
logger.info("creating new Taxon from TaxonName" + nonViralName.getTitleCache());
|
|
1229
|
taxon = Taxon.NewInstance(nonViralName, sec);
|
|
1230
|
}
|
|
1231
|
|
|
1232
|
//citation
|
|
1233
|
Element elCitation = elScope.getChild("Citation",sddNamespace);
|
|
1234
|
if (elCitation != null) {
|
|
1235
|
String refCitation = elCitation.getAttributeValue("ref");
|
|
1236
|
if (! refCitation.equals("")){
|
|
1237
|
citations.put(idCD, refCitation);
|
|
1238
|
}
|
|
1239
|
String location = elCitation.getAttributeValue("location");
|
|
1240
|
if (! location.equals("")){
|
|
1241
|
locations.put(idCD, location);
|
|
1242
|
}
|
|
1243
|
}
|
|
1244
|
return taxon;
|
|
1245
|
}
|
|
1246
|
|
|
1247
|
/**
|
|
1248
|
* @param sddNamespace
|
|
1249
|
* @param taxonDescription
|
|
1250
|
* @param elSummaryData
|
|
1251
|
*/
|
|
1252
|
private void handleSummaryTextData(Namespace sddNamespace,
|
|
1253
|
TaxonDescription taxonDescription, Element elSummaryData) {
|
|
1254
|
String ref;
|
|
1255
|
int k;
|
|
1256
|
// <TextChar ref="c3">
|
|
1257
|
List<Element> elTextChars = elSummaryData.getChildren("TextChar", sddNamespace);
|
|
1258
|
k = 0;
|
|
1259
|
//for each TextChar
|
|
1260
|
for (Element elTextChar : elTextChars){
|
|
1261
|
if ((++k % modCount) == 0){ logger.info("TextChar handled: " + (k-1));}
|
|
1262
|
ref = elTextChar.getAttributeValue("ref");
|
|
1263
|
Feature feature = features.get(ref);
|
|
1264
|
TextData textData = TextData.NewInstance();
|
|
1265
|
textData.setFeature(feature);
|
|
1266
|
|
|
1267
|
// <Content>Free form text</Content>
|
|
1268
|
String content = (String)ImportHelper.getXmlInputValue(elTextChar, "Content",sddNamespace);
|
|
1269
|
textData.putText(content, datasetLanguage);
|
|
1270
|
taxonDescription.addElement(textData);
|
|
1271
|
}
|
|
1272
|
}
|
|
1273
|
|
|
1274
|
/**
|
|
1275
|
* @param sddNamespace
|
|
1276
|
* @param taxonDescription
|
|
1277
|
* @param elSummaryData
|
|
1278
|
*/
|
|
1279
|
private void handleSummaryQuantitativeData(Namespace sddNamespace,
|
|
1280
|
TaxonDescription taxonDescription, Element elSummaryData) {
|
|
1281
|
String ref;
|
|
1282
|
int k;
|
|
1283
|
// <Quantitative ref="c2">
|
|
1284
|
List<Element> elQuantitatives = elSummaryData.getChildren("Quantitative", sddNamespace);
|
|
1285
|
k = 0;
|
|
1286
|
//for each Quantitative
|
|
1287
|
for (Element elQuantitative : elQuantitatives){
|
|
1288
|
if ((++k % modCount) == 0){ logger.warn("Quantitative handled: " + (k-1));}
|
|
1289
|
ref = elQuantitative.getAttributeValue("ref");
|
|
1290
|
Feature feature = features.get(ref);
|
|
1291
|
QuantitativeData quantitativeData = QuantitativeData.NewInstance();
|
|
1292
|
quantitativeData.setFeature(feature);
|
|
1293
|
|
|
1294
|
MeasurementUnit unit = units.get(ref);
|
|
1295
|
String prefix = defaultUnitPrefixes.get(ref);
|
|
1296
|
if (unit != null) {
|
|
1297
|
String u = unit.getLabel();
|
|
1298
|
if (prefix != null) {
|
|
1299
|
u = prefix + u;
|
|
1300
|
}
|
|
1301
|
unit.setLabel(u);
|
|
1302
|
quantitativeData.setUnit(unit);
|
|
1303
|
}
|
|
1304
|
|
|
1305
|
// <Measure type="Min" value="2.3"/>
|
|
1306
|
List<Element> elMeasures = elQuantitative.getChildren("Measure", sddNamespace);
|
|
1307
|
int l = 0;
|
|
1308
|
|
|
1309
|
//for each State
|
|
1310
|
for (Element elMeasure : elMeasures){
|
|
1311
|
if ((++l % modCount) == 0){ logger.info("States handled: " + (l-1));}
|
|
1312
|
String type = elMeasure.getAttributeValue("type");
|
|
1313
|
String value = elMeasure.getAttributeValue("value");
|
|
1314
|
if (value.contains(",")) {
|
|
1315
|
value = value.replace(',', '.');
|
|
1316
|
}
|
|
1317
|
Float v = Float.parseFloat(value);
|
|
1318
|
//Float v = new Float(0);
|
|
1319
|
StatisticalMeasure t = null;
|
|
1320
|
if (type.equals("Min")) {
|
|
1321
|
t = StatisticalMeasure.MIN();
|
|
1322
|
} else if (type.equals("Mean")) {
|
|
1323
|
t = StatisticalMeasure.AVERAGE();
|
|
1324
|
} else if (type.equals("Max")) {
|
|
1325
|
t = StatisticalMeasure.MAX();
|
|
1326
|
} else if (type.equals("SD")) {
|
|
1327
|
t = StatisticalMeasure.STANDARD_DEVIATION();
|
|
1328
|
} else if (type.equals("N")) {
|
|
1329
|
t = StatisticalMeasure.SAMPLE_SIZE();
|
|
1330
|
} else if (type.equals("UMethLower")) {
|
|
1331
|
t = StatisticalMeasure.TYPICAL_LOWER_BOUNDARY();
|
|
1332
|
} else if (type.equals("UMethUpper")) {
|
|
1333
|
t = StatisticalMeasure.TYPICAL_UPPER_BOUNDARY();
|
|
1334
|
} else if (type.equals("Var")) {
|
|
1335
|
t = StatisticalMeasure.VARIANCE();
|
|
1336
|
} else {
|
|
1337
|
t = StatisticalMeasure.NewInstance(type,type,type);
|
|
1338
|
statisticalMeasures.add(t);
|
|
1339
|
}
|
|
1340
|
|
|
1341
|
StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance();
|
|
1342
|
statisticalValue.setValue(v);
|
|
1343
|
statisticalValue.setType(t);
|
|
1344
|
quantitativeData.addStatisticalValue(statisticalValue);
|
|
1345
|
featureData.add(statisticalValue);
|
|
1346
|
}
|
|
1347
|
taxonDescription.addElement(quantitativeData);
|
|
1348
|
}
|
|
1349
|
}
|
|
1350
|
|
|
1351
|
/**
|
|
1352
|
* @param sddNamespace
|
|
1353
|
* @param taxonDescription
|
|
1354
|
* @param elSummaryData
|
|
1355
|
*/
|
|
1356
|
private void handleSummaryCategoricalData(Namespace sddNamespace,
|
|
1357
|
TaxonDescription taxonDescription, Element elSummaryData) {
|
|
1358
|
String ref;
|
|
1359
|
// <Categorical ref="c4">
|
|
1360
|
List<Element> elCategoricals = elSummaryData.getChildren("Categorical", sddNamespace);
|
|
1361
|
int k = 0;
|
|
1362
|
//for each Categorical
|
|
1363
|
for (Element elCategorical : elCategoricals){
|
|
1364
|
if ((++k % modCount) == 0){ logger.warn("Categorical handled: " + (k-1));}
|
|
1365
|
ref = elCategorical.getAttributeValue("ref");
|
|
1366
|
Feature feature = features.get(ref);
|
|
1367
|
CategoricalData categoricalData = CategoricalData.NewInstance();
|
|
1368
|
categoricalData.setFeature(feature);
|
|
1369
|
|
|
1370
|
// <State ref="s3"/>
|
|
1371
|
List<Element> elStates = elCategorical.getChildren("State", sddNamespace);
|
|
1372
|
int l = 0;
|
|
1373
|
|
|
1374
|
//for each State
|
|
1375
|
for (Element elState : elStates){
|
|
1376
|
if ((++l % modCount) == 0){ logger.info("States handled: " + (l-1));}
|
|
1377
|
ref = elState.getAttributeValue("ref");
|
|
1378
|
State state = states.get(ref);
|
|
1379
|
if (state != null) {
|
|
1380
|
StateData stateData = StateData.NewInstance();
|
|
1381
|
stateData.setState(state);
|
|
1382
|
List<Element> elModifiers = elState.getChildren("Modifier", sddNamespace);
|
|
1383
|
for (Element elModifier : elModifiers){
|
|
1384
|
ref = elModifier.getAttributeValue("ref");
|
|
1385
|
Modifier modifier = modifiers.get(ref);
|
|
1386
|
if (modifier != null) {
|
|
1387
|
stateData.addModifier(modifier);
|
|
1388
|
}
|
|
1389
|
}
|
|
1390
|
categoricalData.addState(stateData);
|
|
1391
|
}
|
|
1392
|
taxonDescription.addElement(categoricalData);
|
|
1393
|
}
|
|
1394
|
}
|
|
1395
|
}
|
|
1396
|
|
|
1397
|
// imports the persons associated with the dataset creation, modification, related publications
|
|
1398
|
protected void importAgents(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
|
|
1399
|
// <Agents>
|
|
1400
|
logger.info("start Agents ...");
|
|
1401
|
Element elAgents = elDataset.getChild("Agents",sddNamespace);
|
|
1402
|
if (elAgents != null) {
|
|
1403
|
// <Agent id="a1">
|
|
1404
|
List <Element> listAgents = elAgents.getChildren("Agent", sddNamespace);
|
|
1405
|
int j = 0;
|
|
1406
|
//for each Agent
|
|
1407
|
for (Element elAgent : listAgents){
|
|
1408
|
|
|
1409
|
try {
|
|
1410
|
|
|
1411
|
String idA = elAgent.getAttributeValue("id");
|
|
1412
|
|
|
1413
|
// <Representation>
|
|
1414
|
// <Label>Kevin Thiele</Label>
|
|
1415
|
// <Detail role="Description">Ali Baba is also known as r.a.m.</Detail>
|
|
1416
|
// </Representation>
|
|
1417
|
Person person = Person.NewInstance();
|
|
1418
|
importRepresentation(elAgent, sddNamespace, person, idA, sddConfig);
|
|
1419
|
person.addSource(IdentifiableSource.NewInstance(idA, "Agent"));
|
|
1420
|
|
|
1421
|
/*XIM <Links>
|
|
1422
|
Element elLinks = elAgent.getChild("Links",sddNamespace);
|
|
1423
|
|
|
1424
|
if (elLinks != null) {
|
|
1425
|
|
|
1426
|
// <Link rel="Alternate" href="http://www.diversitycampus.net/people/hagedorn"/>
|
|
1427
|
List<Element> listLinks = elLinks.getChildren("Link", sddNamespace);
|
|
1428
|
int k = 0;
|
|
1429
|
//for each Link
|
|
1430
|
for (Element elLink : listLinks){
|
|
1431
|
|
|
1432
|
try {
|
|
1433
|
|
|
1434
|
String rel = elLink.getAttributeValue("rel");
|
|
1435
|
String href = elLink.getAttributeValue("href");
|
|
1436
|
|
|
1437
|
Media link = Media.NewInstance();
|
|
1438
|
MediaRepresentation mr = MediaRepresentation.NewInstance();
|
|
1439
|
mr.addRepresentationPart(MediaRepresentationPart.NewInstance(href, null));
|
|
1440
|
link.addRepresentation(mr);
|
|
1441
|
person.addMedia(link);
|
|
1442
|
|
|
1443
|
} catch (Exception e) {
|
|
1444
|
//FIXME
|
|
1445
|
logger.warn("Import of Link " + k + " failed.");
|
|
1446
|
success = false;
|
|
1447
|
}
|
|
1448
|
|
|
1449
|
if ((++k % modCount) == 0){ logger.info("Links handled: " + k);}
|
|
1450
|
|
|
1451
|
}
|
|
1452
|
}
|
|
1453
|
*/
|
|
1454
|
if (authors.containsKey(idA)) {
|
|
1455
|
authors.put(idA,person);
|
|
1456
|
}
|
|
1457
|
|
|
1458
|
if (editors.containsKey(idA)) {
|
|
1459
|
editors.put(idA, person);
|
|
1460
|
}
|
|
1461
|
|
|
1462
|
} catch (Exception e) {
|
|
1463
|
//FIXME
|
|
1464
|
logger.warn("Import of Agent " + j + " failed.");
|
|
1465
|
success = false;
|
|
1466
|
}
|
|
1467
|
|
|
1468
|
if ((++j % modCount) == 0){ logger.info("Agents handled: " + j);}
|
|
1469
|
|
|
1470
|
}
|
|
1471
|
}
|
|
1472
|
}
|
|
1473
|
|
|
1474
|
// imports publications related with the data set
|
|
1475
|
protected void importPublications(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
|
|
1476
|
/* <Publications>
|
|
1477
|
<Publication id="p112">
|
|
1478
|
<Representation>
|
|
1479
|
<Label>Gee, X. & Haa, Y. (2003). How to be happy in five minutes. Instant Gratifications, Palm Beach.</Label>
|
|
1480
|
</Representation>
|
|
1481
|
<Links>
|
|
1482
|
<Link rel="BasedOn" href="doi:10.1992/32311"/>
|
|
1483
|
<Link rel="Alternate" href="http://some.service.net/providing/bibliographic.data"/>
|
|
1484
|
</Links>
|
|
1485
|
</Publications>
|
|
1486
|
*/
|
|
1487
|
logger.info("start Publications ...");
|
|
1488
|
Element elPublications = elDataset.getChild("Publications",sddNamespace);
|
|
1489
|
|
|
1490
|
if (elPublications != null) {
|
|
1491
|
List<Element> listPublications = elPublications.getChildren("Publication", sddNamespace);
|
|
1492
|
int j = 0;
|
|
1493
|
for (Element elPublication : listPublications){
|
|
1494
|
|
|
1495
|
try {
|
|
1496
|
|
|
1497
|
String idP = elPublication.getAttributeValue("id");
|
|
1498
|
ReferenceBase publication = ReferenceFactory.newArticle();
|
|
1499
|
importRepresentation(elPublication, sddNamespace, publication, idP, sddConfig);
|
|
1500
|
|
|
1501
|
publications.put(idP,publication);
|
|
1502
|
|
|
1503
|
} catch (Exception e) {
|
|
1504
|
logger.warn("Import of Publication " + j + " failed.");
|
|
1505
|
success = false;
|
|
1506
|
}
|
|
1507
|
|
|
1508
|
if ((++j % modCount) == 0){ logger.info("Publications handled: " + j);}
|
|
1509
|
|
|
1510
|
}
|
|
1511
|
}
|
|
1512
|
}
|
|
1513
|
|
|
1514
|
// imports media objects such as images //FIXME check mediaobj
|
|
1515
|
protected void importMediaObjects(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
|
|
1516
|
// <MediaObjects>
|
|
1517
|
logger.info("start MediaObjects ...");
|
|
1518
|
Element elMediaObjects = elDataset.getChild("MediaObjects",sddNamespace);
|
|
1519
|
|
|
1520
|
if (elMediaObjects != null) {
|
|
1521
|
// <MediaObject id="m1">
|
|
1522
|
List<Element> listMediaObjects = elMediaObjects.getChildren("MediaObject", sddNamespace);
|
|
1523
|
int j = 0;
|
|
1524
|
for (Element elMO : listMediaObjects){
|
|
1525
|
|
|
1526
|
String id = "";
|
|
1527
|
|
|
1528
|
try {
|
|
1529
|
String idMO = elMO.getAttributeValue("id");
|
|
1530
|
id = idMO;
|
|
1531
|
|
|
1532
|
// <Representation>
|
|
1533
|
// <Label>Image description, e.g. to be used for alt-attribute in html.</Label>
|
|
1534
|
// </Representation>
|
|
1535
|
Media media = Media.NewInstance();
|
|
1536
|
importRepresentation(elMO, sddNamespace, media, idMO, sddConfig);
|
|
1537
|
|
|
1538
|
// <Type>Image</Type>
|
|
1539
|
// <Source href="http://test.edu/test.jpg"/>
|
|
1540
|
String type = (String)ImportHelper.getXmlInputValue(elMO,"Type",sddNamespace);
|
|
1541
|
|
|
1542
|
if ((type != null) && (type.equals("Image"))) {
|
|
1543
|
Element elSource = elMO.getChild("Source",sddNamespace);
|
|
1544
|
String href = elSource.getAttributeValue("href");
|
|
1545
|
|
|
1546
|
ImageMetaData imageMetaData = ImageMetaData.newInstance();
|
|
1547
|
ImageFile image = null;
|
|
1548
|
if (href.substring(0,7).equals("http://")) {
|
|
1549
|
try{
|
|
1550
|
URL url = new URL(href);
|
|
1551
|
|
|
1552
|
imageMetaData.readMetaData(url.toURI(), 0);
|
|
1553
|
image = ImageFile.NewInstance(url.toString(), null, imageMetaData);
|
|
1554
|
} catch (MalformedURLException e) {
|
|
1555
|
logger.error("Malformed URL", e);
|
|
1556
|
}
|
|
1557
|
} else {
|
|
1558
|
String sns = sddConfig.getSourceNameString();
|
|
1559
|
File f = new File(sns);
|
|
1560
|
File parent = f.getParentFile();
|
|
1561
|
String fi = href;
|
|
1562
|
//String fi = parent.toString() + File.separator + href; //TODO erase file:/
|
|
1563
|
File file = new File(fi);
|
|
1564
|
imageMetaData.readMetaData(file.toURI(), 0);
|
|
1565
|
image = ImageFile.NewInstance(file.toString(), null, imageMetaData);
|
|
1566
|
}
|
|
1567
|
MediaRepresentation representation = MediaRepresentation.NewInstance(imageMetaData.getMimeType(), null);
|
|
1568
|
representation.addRepresentationPart(image);
|
|
1569
|
|
|
1570
|
media.addRepresentation(representation);
|
|
1571
|
|
|
1572
|
ArrayList<CdmBase> lcb = (ArrayList<CdmBase>) mediaObject_ListCdmBase.get(idMO);
|
|
1573
|
if (lcb != null) {
|
|
1574
|
for (int k = 0; k < lcb.size(); k++) {
|
|
1575
|
if (lcb.get(k) instanceof DefinedTermBase) {
|
|
1576
|
DefinedTermBase dtb = (DefinedTermBase) lcb.get(k);
|
|
1577
|
// if (lcb.get(0) instanceof DefinedTermBase) {
|
|
1578
|
// DefinedTermBase dtb = (DefinedTermBase) lcb.get(0);
|
|
1579
|
// if (dtb!=null) {
|
|
1580
|
// if (k == 0) {
|
|
1581
|
dtb.addMedia(media);
|
|
1582
|
//System.out.println(dtb.getLabel());
|
|
1583
|
// } else {
|
|
1584
|
// Media me = (Media) media.clone();
|
|
1585
|
// dtb.addMedia(me);
|
|
1586
|
// }
|
|
1587
|
// }
|
|
1588
|
} else if (lcb.get(k) instanceof ReferenceBase) {
|
|
1589
|
ReferenceBase rb = (ReferenceBase) lcb.get(k);
|
|
1590
|
//} else if (lcb.get(0) instanceof ReferenceBase) {
|
|
1591
|
//ReferenceBase rb = (ReferenceBase) lcb.get(0);
|
|
1592
|
// rb.setTitleCache(label);
|
|
1593
|
// if (rb!=null) {
|
|
1594
|
// if (k == 0) {
|
|
1595
|
rb.addMedia(media);
|
|
1596
|
//System.out.println(rb.getTitle());
|
|
1597
|
// } else {
|
|
1598
|
// Media me = (Media) media.clone();
|
|
1599
|
// rb.addMedia(me);
|
|
1600
|
// }
|
|
1601
|
// }
|
|
1602
|
}/* else if (lcb.get(k) instanceof TaxonNameBase){
|
|
1603
|
TaxonNameBase tb = (TaxonNameBase) lcb.get(k);
|
|
1604
|
tb.addMedia(media);
|
|
1605
|
}*/
|
|
1606
|
}
|
|
1607
|
}
|
|
1608
|
}
|
|
1609
|
|
|
1610
|
} catch (Exception e) {
|
|
1611
|
//FIXME
|
|
1612
|
logger.warn("Could not attach MediaObject " + j + "(SDD: " + id + ") to several objects.");
|
|
1613
|
success = false;
|
|
1614
|
}
|
|
1615
|
|
|
1616
|
if ((++j % modCount) == 0){ logger.info("MediaObjects handled: " + j);
|
|
1617
|
|
|
1618
|
}
|
|
1619
|
}
|
|
1620
|
}
|
|
1621
|
}
|
|
1622
|
|
|
1623
|
// imports the <DescriptiveConcepts> block ; DescriptiveConcepts are used as nodes in CharacterTrees and Characters as leaves
|
|
1624
|
// but since Modifiers can be linked to DescriptiveConcepts they are stored as features with a particular Marker
|
|
1625
|
protected void importDescriptiveConcepts(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig){
|
|
1626
|
/* <DescriptiveConcepts>
|
|
1627
|
<DescriptiveConcept id="dc0">
|
|
1628
|
<Representation>
|
|
1629
|
<Label>Fixed set of modifiers supported in Lucid3</Label>
|
|
1630
|
</Representation>
|
|
1631
|
<Modifiers>
|
|
1632
|
<Modifier id="mod1">
|
|
1633
|
<Representation>
|
|
1634
|
<Label>rarely</Label>
|
|
1635
|
</Representation>
|
|
1636
|
<ModifierClass>Frequency</ModifierClass>
|
|
1637
|
<ProportionRange lowerestimate="0.0" upperestimate="0.25"/>
|
|
1638
|
</Modifier>
|
|
1639
|
</Modifiers>
|
|
1640
|
</DescriptiveConcept>
|
|
1641
|
</DescriptiveConcepts>
|
|
1642
|
*/
|
|
1643
|
logger.info("start DescriptiveConcepts ...");
|
|
1644
|
Element elDescriptiveConcepts = elDataset.getChild("DescriptiveConcepts",sddNamespace);
|
|
1645
|
if (elDescriptiveConcepts != null) {
|
|
1646
|
List<Element> listDescriptiveConcepts = elDescriptiveConcepts.getChildren("DescriptiveConcept", sddNamespace);
|
|
1647
|
int j = 0;
|
|
1648
|
|
|
1649
|
for (Element elDescriptiveConcept : listDescriptiveConcepts){
|
|
1650
|
try {
|
|
1651
|
String id = elDescriptiveConcept.getAttributeValue("id");
|
|
1652
|
Feature feature = Feature.NewInstance();
|
|
1653
|
feature.setKindOf(Feature.DESCRIPTION());
|
|
1654
|
if (!id.equals("")) {
|
|
1655
|
// <Representation>
|
|
1656
|
// <Label>Body</Label>
|
|
1657
|
importRepresentation(elDescriptiveConcept, sddNamespace, feature, id, sddConfig);
|
|
1658
|
features.put(id, feature);
|
|
1659
|
getTermService().save(feature);//XIM
|
|
1660
|
descriptiveConcepts.add(feature);
|
|
1661
|
// imports the modifiers
|
|
1662
|
Element elModifiers = elDescriptiveConcept.getChild("Modifiers", sddNamespace);
|
|
1663
|
if (elModifiers !=null){
|
|
1664
|
List<Element> listModifiers = elModifiers.getChildren("Modifier", sddNamespace);
|
|
1665
|
TermVocabulary<Modifier> termVocabularyState = new TermVocabulary<Modifier>();
|
|
1666
|
for (Element elModifier : listModifiers) {
|
|
1667
|
Modifier modif = Modifier.NewInstance();
|
|
1668
|
String idmod = elModifier.getAttributeValue("id");
|
|
1669
|
importRepresentation(elModifier, sddNamespace, modif, idmod, sddConfig);
|
|
1670
|
termVocabularyState.addTerm(modif);
|
|
1671
|
//termVocabularyStates.add(termVocabularyState);
|
|
1672
|
getVocabularyService().save(termVocabularyState);//XIM
|
|
1673
|
modifiers.put(idmod, modif);
|
|
1674
|
}
|
|
1675
|
feature.addRecommendedModifierEnumeration(termVocabularyState);
|
|
1676
|
}
|
|
1677
|
|
|
1678
|
}
|
|
1679
|
}
|
|
1680
|
catch (Exception e) {
|
|
1681
|
logger.warn("Import of DescriptiveConcept " + j + " failed.");
|
|
1682
|
}
|
|
1683
|
if ((++j % modCount) == 0){ logger.info("DescriptiveConcepts handled: " + j);}
|
|
1684
|
|
|
1685
|
}
|
|
1686
|
}
|
|
1687
|
}
|
|
1688
|
|
|
1689
|
// imports the <CharacterTrees> block
|
|
1690
|
protected void importCharacterTrees(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
|
|
1691
|
// <CharacterTrees>
|
|
1692
|
logger.info("start CharacterTrees ...");
|
|
1693
|
Element elCharacterTrees = elDataset.getChild("CharacterTrees",sddNamespace);
|
|
1694
|
|
|
1695
|
if (elCharacterTrees != null) {
|
|
1696
|
List<Element> listCharacterTrees = elCharacterTrees.getChildren("CharacterTree", sddNamespace);
|
|
1697
|
int j = 0;
|
|
1698
|
for (Element elCharacterTree : listCharacterTrees){
|
|
1699
|
try {
|
|
1700
|
Element elRepresentation = elCharacterTree.getChild("Representation",sddNamespace);
|
|
1701
|
String label = (String)ImportHelper.getXmlInputValue(elRepresentation,"Label",sddNamespace);
|
|
1702
|
//Element elDesignedFor = elCharacterTree.getChild("DesignedFor",sddNamespace);//TODO ?
|
|
1703
|
|
|
1704
|
FeatureTree feattree = FeatureTree.NewInstance();
|
|
1705
|
importRepresentation(elCharacterTree, sddNamespace, feattree, "", sddConfig);
|
|
1706
|
FeatureNode root = feattree.getRoot();
|
|
1707
|
List<Element> listelNodes = elCharacterTree.getChildren("Nodes", sddNamespace);
|
|
1708
|
|
|
1709
|
//Nodes of CharacterTrees in SDD always refer to DescriptiveConcepts
|
|
1710
|
for (Element elNodes : listelNodes) {
|
|
1711
|
List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
|
|
1712
|
if (listNodes != null) {
|
|
1713
|
for (Element elNode : listNodes){
|
|
1714
|
String idN = elNode.getAttributeValue("id");
|
|
1715
|
FeatureNode fn = null;
|
|
1716
|
Feature dc = null;
|
|
1717
|
if (idN!=null) {
|
|
1718
|
// DescriptiveConcepts are used as nodes in CharacterTrees
|
|
1719
|
Element elDescriptiveConcept = elNode.getChild("DescriptiveConcept", sddNamespace);
|
|
1720
|
if (elDescriptiveConcept != null){
|
|
1721
|
String refDC = elDescriptiveConcept.getAttributeValue("ref");
|
|
1722
|
dc = features.get(refDC);
|
|
1723
|
fn = FeatureNode.NewInstance(dc);
|
|
1724
|
}
|
|
1725
|
if (fn==null){
|
|
1726
|
fn = FeatureNode.NewInstance();
|
|
1727
|
}
|
|
1728
|
Element elParent = elNode.getChild("Parent", sddNamespace);
|
|
1729
|
// in SDD links between Nodes are referenced by the <Parent> tag
|
|
1730
|
if (elParent!=null){
|
|
1731
|
String refP = elParent.getAttributeValue("ref");
|
|
1732
|
if (refP!=null) {
|
|
1733
|
FeatureNode parent = featureNodes.get(refP);
|
|
1734
|
if (parent==null){
|
|
1735
|
root.addChild(fn); // if no parent found or the reference is broken, add the node to the root of the tree
|
|
1736
|
}
|
|
1737
|
else {
|
|
1738
|
parent.addChild(fn);
|
|
1739
|
}
|
|
1740
|
}
|
|
1741
|
}
|
|
1742
|
else {
|
|
1743
|
root.addChild(fn); // if no parent found or the reference is broken, add the node to the root of the tree
|
|
1744
|
}
|
|
1745
|
}
|
|
1746
|
featureNodes.put(idN, fn);
|
|
1747
|
}
|
|
1748
|
}
|
|
1749
|
|
|
1750
|
// Leaves of CharacterTrees in SDD are always CharNodes (referring to Characters)
|
|
1751
|
List<Element> listCharNodes = elNodes.getChildren("CharNode", sddNamespace);
|
|
1752
|
if (listCharNodes != null) {
|
|
1753
|
for (Element elCharNode : listCharNodes){
|
|
1754
|
Element elParent = elCharNode.getChild("Parent", sddNamespace);
|
|
1755
|
Element elCharacter = elCharNode.getChild("Character", sddNamespace);
|
|
1756
|
FeatureNode fn = FeatureNode.NewInstance();
|
|
1757
|
if (elParent!=null){
|
|
1758
|
String refP = elParent.getAttributeValue("ref");
|
|
1759
|
if ((refP!=null)&&(!refP.equals(""))) {
|
|
1760
|
FeatureNode parent = featureNodes.get(refP);
|
|
1761
|
if (parent==null){
|
|
1762
|
parent = root; // if no parent found or the reference is broken, add the node to the root of the tree
|
|
1763
|
}
|
|
1764
|
parent.addChild(fn);
|
|
1765
|
}
|
|
1766
|
}
|
|
1767
|
String refC = elCharacter.getAttributeValue("ref");
|
|
1768
|
if ((refC!=null)&&(!refC.equals(""))){
|
|
1769
|
Feature character = features.get(refC);
|
|
1770
|
fn.setFeature(character);
|
|
1771
|
featureNodes.put(refC, fn);
|
|
1772
|
}
|
|
1773
|
}
|
|
1774
|
}
|
|
1775
|
}
|
|
1776
|
featureTrees.add(feattree);
|
|
1777
|
}
|
|
1778
|
|
|
1779
|
catch (Exception e) {
|
|
1780
|
logger.warn("Import of Character tree " + j + " failed.");
|
|
1781
|
success = false;
|
|
1782
|
}
|
|
1783
|
if ((++j % modCount) == 0){ logger.info("CharacterTrees handled: " + j);}
|
|
1784
|
|
|
1785
|
}
|
|
1786
|
|
|
1787
|
}
|
|
1788
|
}
|
|
1789
|
|
|
1790
|
// imports the <TaxonHierarchies> block
|
|
1791
|
protected void importTaxonHierarchies(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig, boolean success){
|
|
1792
|
|
|
1793
|
logger.info("start TaxonHierarchies ...");
|
|
1794
|
Element elTaxonHierarchies = elDataset.getChild("TaxonHierarchies",sddNamespace);
|
|
1795
|
|
|
1796
|
if (elTaxonHierarchies != null) {
|
|
1797
|
List<Element> listTaxonHierarchies = elTaxonHierarchies.getChildren("TaxonHierarchy", sddNamespace);
|
|
1798
|
int j = 0;
|
|
1799
|
for (Element elTaxonHierarchy : listTaxonHierarchies){
|
|
1800
|
try {
|
|
1801
|
Element elRepresentation = elTaxonHierarchy.getChild("Representation",sddNamespace);
|
|
1802
|
String label = (String)ImportHelper.getXmlInputValue(elRepresentation,"Label",sddNamespace);
|
|
1803
|
TaxonomicTree taxonomicTree = TaxonomicTree.NewInstance(label);
|
|
1804
|
importRepresentation(elTaxonHierarchy, sddNamespace, taxonomicTree, "", sddConfig);
|
|
1805
|
|
|
1806
|
Set<TaxonNode> root = taxonomicTree.getChildNodes();
|
|
1807
|
Element elNodes = elTaxonHierarchy.getChild("Nodes", sddNamespace); // There can be only one <Nodes> block for TaxonHierarchies
|
|
1808
|
List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
|
|
1809
|
|
|
1810
|
for (Element elNode : listNodes){
|
|
1811
|
String idN = elNode.getAttributeValue("id");
|
|
1812
|
TaxonNameBase tnb = null;
|
|
1813
|
if (!idN.equals("")) {
|
|
1814
|
Element elTaxonName = elNode.getChild("TaxonName", sddNamespace);
|
|
1815
|
String refTN = elTaxonName.getAttributeValue("ref");
|
|
1816
|
tnb = taxonNameBases.get(refTN);
|
|
1817
|
Taxon taxon = (Taxon) tnb.getTaxa().iterator().next() ;
|
|
1818
|
Element elParent = elNode.getChild("Parent", sddNamespace);
|
|
1819
|
if (elParent!=null){
|
|
1820
|
String refP = elParent.getAttributeValue("ref");
|
|
1821
|
if (!refP.equals("")) {
|
|
1822
|
TaxonNode parent = taxonNodes.get(refP);
|
|
1823
|
TaxonNode child = parent.addChildTaxon(taxon, sec, "", Synonym.NewInstance(tnb, sec));
|
|
1824
|
taxonNodes.put(idN,child);
|
|
1825
|
}
|
|
1826
|
}
|
|
1827
|
else {
|
|
1828
|
TaxonNode tn = taxonomicTree.addChildTaxon(taxon, sec, "", Synonym.NewInstance(tnb, sec)); // if no parent found or the reference is broken, add the node to the root of the tree
|
|
1829
|
taxonNodes.put(idN,tn);
|
|
1830
|
}
|
|
1831
|
}
|
|
1832
|
}
|
|
1833
|
|
|
1834
|
taxonomicTrees.add(taxonomicTree);
|
|
1835
|
}
|
|
1836
|
|
|
1837
|
catch (Exception e) {
|
|
1838
|
//FIXME
|
|
1839
|
logger.warn("Import of Taxon Hierarchy " + j + " failed.");
|
|
1840
|
success = false;
|
|
1841
|
}
|
|
1842
|
|
|
1843
|
if ((++j % modCount) == 0){ logger.info("TaxonHierarchies handled: " + j);}
|
|
1844
|
|
|
1845
|
}
|
|
1846
|
|
|
1847
|
}
|
|
1848
|
}
|
|
1849
|
|
|
1850
|
|
|
1851
|
// imports the <GeographicAreas> block
|
|
1852
|
protected void importGeographicAreas(Element elDataset, Namespace sddNamespace, SDDImportConfigurator sddConfig) {
|
|
1853
|
Element elGeographicAreas = elDataset.getChild("GeographicAreas",sddNamespace);
|
|
1854
|
if (elGeographicAreas != null) {
|
|
1855
|
List<Element> listGeographicAreas = elGeographicAreas.getChildren("GeographicArea", sddNamespace);
|
|
1856
|
int j = 0;
|
|
1857
|
|
|
1858
|
for (Element elGeographicArea : listGeographicAreas){
|
|
1859
|
|
|
1860
|
String id = elGeographicArea.getAttributeValue("id");
|
|
1861
|
NamedArea na = new NamedArea();
|
|
1862
|
importRepresentation(elGeographicArea, sddNamespace, na, id, sddConfig);
|
|
1863
|
namedAreas.put(id,na);
|
|
1864
|
}
|
|
1865
|
if ((++j % modCount) == 0){ logger.info("GeographicAreas handled: " + j);}
|
|
1866
|
}
|
|
1867
|
}
|
|
1868
|
}
|