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/**
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*
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*/
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package eu.etaxonomy.cdm.io.tcs;
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import java.util.Calendar;
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import java.util.List;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import org.jdom.Attribute;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.INameService;
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import eu.etaxonomy.cdm.api.service.IReferenceService;
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import eu.etaxonomy.cdm.common.XmlHelp;
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import eu.etaxonomy.cdm.io.common.CdmIoBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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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.common.MapWrapper;
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import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Generic;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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*
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*/
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public class TcsReferenceIO extends CdmIoBase implements ICdmIO {
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private static final Logger logger = Logger.getLogger(TcsReferenceIO.class);
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private static int modCount = 1000;
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public TcsReferenceIO(){
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super();
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}
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@Override
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public boolean doCheck(IImportConfigurator config){
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boolean result = true;
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result &= checkArticlesWithoutJournal(config);
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result &= checkPartOfJournal(config);
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return result;
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}
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private static boolean checkArticlesWithoutJournal(IImportConfigurator bmiConfig){
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try {
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boolean result = true;
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// Source source = bmiConfig.getSource();
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// String strQueryArticlesWithoutJournal = "SELECT Reference.RefId, InRef.RefId AS InRefID, Reference.RefCategoryFk, InRef.RefCategoryFk AS InRefCatFk, Reference.RefCache, Reference.NomRefCache, Reference.Title, RefCategory.RefCategoryAbbrev, InRefCategory.RefCategoryAbbrev AS InRefCat, InRef.Title AS InRefTitle " +
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// " FROM Reference INNER JOIN Reference AS InRef ON Reference.InRefFk = InRef.RefId INNER JOIN RefCategory ON Reference.RefCategoryFk = RefCategory.RefCategoryId INNER JOIN RefCategory AS InRefCategory ON InRef.RefCategoryFk = InRefCategory.RefCategoryId " +
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// " WHERE (Reference.RefCategoryFk = 1) AND (InRef.RefCategoryFk <> 9) ";
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// ResultSet resulSetarticlesWithoutJournal = source.getResultSet(strQueryArticlesWithoutJournal);
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// boolean firstRow = true;
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// while (resulSetarticlesWithoutJournal.next()){
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// if (firstRow){
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// System.out.println("========================================================");
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// logger.warn("There are Articles with wrong inRef type!");
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// System.out.println("========================================================");
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// }
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// int refId = resulSetarticlesWithoutJournal.getInt("RefId");
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// int categoryFk = resulSetarticlesWithoutJournal.getInt("RefCategoryFk");
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// String cat = resulSetarticlesWithoutJournal.getString("RefCategoryAbbrev");
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// int inRefFk = resulSetarticlesWithoutJournal.getInt("InRefId");
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// int inRefCategoryFk = resulSetarticlesWithoutJournal.getInt("InRefCatFk");
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// String inRefCat = resulSetarticlesWithoutJournal.getString("InRefCat");
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// String refCache = resulSetarticlesWithoutJournal.getString("RefCache");
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// String nomRefCache = resulSetarticlesWithoutJournal.getString("nomRefCache");
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// String title = resulSetarticlesWithoutJournal.getString("title");
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// String inRefTitle = resulSetarticlesWithoutJournal.getString("InRefTitle");
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//
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// System.out.println("RefID:" + refId + "\n cat: " + cat +
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// "\n refCache: " + refCache + "\n nomRefCache: " + nomRefCache + "\n title: " + title +
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// "\n inRefFk: " + inRefFk + "\n inRefCategory: " + inRefCat +
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// "\n inRefTitle: " + inRefTitle );
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// result = firstRow = false;
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// }
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//
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return result;
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} catch (Exception e) {
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e.printStackTrace();
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return false;
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}
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}
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private boolean checkPartOfJournal(IImportConfigurator bmiConfig){
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try {
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boolean result = true;
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// Source source = bmiConfig.getSource();
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// String strQueryPartOfJournal = "SELECT Reference.RefId, InRef.RefId AS InRefID, Reference.RefCategoryFk, InRef.RefCategoryFk AS InRefCatFk, Reference.RefCache, Reference.NomRefCache, Reference.Title, RefCategory.RefCategoryAbbrev, InRefCategory.RefCategoryAbbrev AS InRefCat, InRef.Title AS InRefTitle " +
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// " FROM Reference INNER JOIN Reference AS InRef ON Reference.InRefFk = InRef.RefId INNER JOIN RefCategory ON Reference.RefCategoryFk = RefCategory.RefCategoryId INNER JOIN RefCategory AS InRefCategory ON InRef.RefCategoryFk = InRefCategory.RefCategoryId " +
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// " WHERE (Reference.RefCategoryFk = 2) AND (InRef.RefCategoryFk = 9) ";
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// ResultSet rs = source.getResultSet(strQueryPartOfJournal);
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// boolean firstRow = true;
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// while (rs.next()){
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// if (firstRow){
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// System.out.println("========================================================");
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// logger.warn("There are part-of-references that have a Journal as in-reference!");
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// System.out.println("========================================================");
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// }
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// int refId = rs.getInt("RefId");
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// int categoryFk = rs.getInt("RefCategoryFk");
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// String cat = rs.getString("RefCategoryAbbrev");
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// int inRefFk = rs.getInt("InRefId");
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// int inRefCategoryFk = rs.getInt("InRefCatFk");
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// String inRefCat = rs.getString("InRefCat");
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// String refCache = rs.getString("RefCache");
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// String nomRefCache = rs.getString("nomRefCache");
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// String title = rs.getString("title");
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// String inRefTitle = rs.getString("InRefTitle");
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//
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// System.out.println("RefID:" + refId + "\n cat: " + cat +
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// "\n refCache: " + refCache + "\n nomRefCache: " + nomRefCache + "\n title: " + title +
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// "\n inRefFk: " + inRefFk + "\n inRefCategory: " + inRefCat +
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// "\n inRefTitle: " + inRefTitle );
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// result = firstRow = false;
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// }
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//
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return result;
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} catch (Exception e) {
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e.printStackTrace();
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return false;
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}
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}
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@Override
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public boolean doInvoke(IImportConfigurator config, CdmApplicationController cdmApp,
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Map<String, MapWrapper<? extends CdmBase>> stores){
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MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
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MapWrapper<TeamOrPersonBase> authorMap = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.AUTHOR_STORE);
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TcsImportConfigurator tcsConfig = (TcsImportConfigurator)config;
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Element source = tcsConfig.getSourceRoot();
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Element root = tcsConfig.getSourceRoot();
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logger.info("start makeReferences ...");
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String tcsElementName;
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Namespace tcsNamespace;
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String cdmAttrName;
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String value;
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boolean success = true;
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IReferenceService referenceService = cdmApp.getReferenceService();
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MapWrapper<ReferenceBase> referenceStore= new MapWrapper<ReferenceBase>(null);
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//Map<Integer, ReferenceBase> referenceCollectionMap = new HashMap<Integer, ReferenceBase>();
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Namespace rdfNamespace = root.getNamespace();
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String prefix = "tn";
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Namespace taxonNameNamespace = root.getNamespace(prefix);
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prefix = "tc";
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Namespace taxonConceptNamespace = root.getNamespace(prefix);
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prefix = "tcom";
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Namespace commonNamespace = root.getNamespace(prefix);
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prefix = "tpub";
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Namespace publicationNamespace = root.getNamespace(prefix);
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tcsElementName = "PublicationCitation";
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tcsNamespace = publicationNamespace;
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List<Element> elPublicationCitations = root.getChildren(tcsElementName, tcsNamespace);
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int i = 0;
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//for each taxonName
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for (Element elPublicationCitation : elPublicationCitations){
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if ((++i % modCount) == 0){ logger.info("Names handled: " + (i-1));}
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Attribute about = elPublicationCitation.getAttribute("about", rdfNamespace);
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//create TaxonName element
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String strAbout = elPublicationCitation.getAttributeValue("about", rdfNamespace);
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String pages =
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tcsElementName = "publicationType";
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tcsNamespace = publicationNamespace;
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String strPubType = XmlHelp.getChildAttributeValue(elPublicationCitation, tcsElementName, tcsNamespace, "resource", rdfNamespace);
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try {
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ReferenceBase refBase = TcsTransformer.pubTypeStr2PubType(strPubType);
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//attributes
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tcsElementName = "publisher";
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tcsNamespace = publicationNamespace;
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cdmAttrName = "genusOrUninomial";
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success &= ImportHelper.addXmlStringValue(elPublicationCitation, refBase, tcsElementName, tcsNamespace, cdmAttrName);
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tcsElementName = "shortTitle";
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tcsNamespace = publicationNamespace;
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cdmAttrName = "title";
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success &= ImportHelper.addXmlStringValue(elPublicationCitation, refBase, tcsElementName, tcsNamespace, cdmAttrName);
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tcsElementName = "title";
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tcsNamespace = publicationNamespace;
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cdmAttrName = "title";
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success &= ImportHelper.addXmlStringValue(elPublicationCitation, refBase, tcsElementName, tcsNamespace, cdmAttrName);
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tcsElementName = "year";
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tcsNamespace = publicationNamespace;
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cdmAttrName = "year";
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success &= ImportHelper.addXmlStringValue(elPublicationCitation, refBase, tcsElementName, tcsNamespace, cdmAttrName);
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//TODO
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tcsElementName = "year";
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tcsNamespace = publicationNamespace;
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Integer year = null;
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try {
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value = (String)ImportHelper.getXmlInputValue(elPublicationCitation, tcsElementName, tcsNamespace);
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year = Integer.valueOf(value);
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Calendar cal = Calendar.getInstance();
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//FIXME
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cal.set(year, 1, 1);
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if (refBase instanceof StrictReferenceBase){
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StrictReferenceBase ref = (StrictReferenceBase)refBase;
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ref.setDatePublished(TimePeriod.NewInstance(cal));
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}else{
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logger.warn("year not implemented for ReferenceBase type " + ((refBase == null) ? "(null)" : refBase.getClass().getSimpleName()));
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}
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} catch (RuntimeException e) {
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logger.warn("year could not be parsed");
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}
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tcsElementName = "pages";
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tcsNamespace = publicationNamespace;
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cdmAttrName = "pages";
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success &= ImportHelper.addXmlStringValue(elPublicationCitation, refBase, tcsElementName, tcsNamespace, cdmAttrName);
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tcsElementName = "volume";
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tcsNamespace = publicationNamespace;
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cdmAttrName = "volume";
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success &= ImportHelper.addXmlStringValue(elPublicationCitation, refBase, tcsElementName, tcsNamespace, cdmAttrName);
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//Reference
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//TODO
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tcsElementName = "parentPublication";
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tcsNamespace = publicationNamespace;
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String strParent = XmlHelp.getChildAttributeValue(elPublicationCitation, tcsElementName, tcsNamespace, "resource", rdfNamespace);
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ReferenceBase parent = referenceMap.get(strParent);
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if (parent != null){
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logger.warn("parent not yet implemented");
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//TODO refBase.setParent(parent);
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}
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//ImportHelper.setOriginalSource(nameBase, tcsConfig.getSourceReference(), nameId);
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referenceMap.put(strAbout, refBase);
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} catch (UnknownCdmTypeException e) {
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//FIXME
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logger.warn("Name with id " + strAbout + " has unknown type " + strPubType + " and could not be saved.");
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success = false;
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}
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}
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logger.info(i + " names handled");
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referenceService.saveReferenceAll(referenceMap.objects());
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logger.info("end makeReferences ...");
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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(IImportConfigurator config){
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return (config.getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
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}
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}
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