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package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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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.io.common.Source;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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.TaxonBase;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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@Component
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public class FaunaEuropaeaVernacularNamesImport extends FaunaEuropaeaImportBase {
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private static final long serialVersionUID = 168771351441040059L;
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaVernacularNamesImport.class);
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private HashMap<String, Reference> sourceMap = new HashMap<String, Reference>();
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private Reference pesiProject = ReferenceFactory.newDatabase();
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@Override
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protected void doInvoke(FaunaEuropaeaImportState state) {
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int limit = state.getConfig().getLimitSave();
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pesiProject.setTitle("PESI");
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if (state.getConfig().isDoVernacularNames()){
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/* Taxon store for retrieving taxa from and saving taxa to CDM */
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List<TaxonBase> taxonList = null;
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/* UUID store as input for retrieving taxa from CDM */
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Set<UUID> taxonUuids = null;
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/* Store to hold helper objects */
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Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuVernacularNamesMap = null;
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TransactionStatus txStatus = null;
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createSourceMap(state);
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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Source source = fauEuConfig.getSource();
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int i = 0;
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String selectCount =
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" SELECT count(*) ";
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String selectColumns =
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" SELECT vernacularNames.*, Taxon.UUID ";
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String fromClause =
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" FROM vernacularNames INNER JOIN " +
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" Taxon ON vernacularnames.UUID = Taxon.UUID ";
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String orderBy = " ORDER BY vernacularNames.UUID";
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String countQuery =
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selectCount + fromClause;
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String selectQuery =
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selectColumns + fromClause + orderBy;
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if(logger.isInfoEnabled()) { logger.info("Start making vernacular names..."); }
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try {
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ResultSet rs = source.getResultSet(countQuery);
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rs.next();
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int count = rs.getInt(1);
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rs = source.getResultSet(selectQuery);
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if (logger.isInfoEnabled()) {
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logger.info("Number of rows: " + count);
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logger.info("Count Query: " + countQuery);
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logger.info("Select Query: " + selectQuery);
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}
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//int taxonId;
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while (rs.next()) {
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if ((i++ % limit) == 0) {
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txStatus = startTransaction();
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taxonUuids = new HashSet<UUID>(limit);
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fauEuVernacularNamesMap = new HashMap<UUID, FaunaEuropaeaVernacularNamesTaxon>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - vernacular names import transaction started");
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}
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}
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//taxonId = rs.getInt("dis_tax_id");
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String vernameGUID = rs.getString("GUID");
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String vernacularNameString = rs.getString("verName");
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//int taxonFk = rs.getInt("taxonFK");
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int languageFK= rs.getInt("languageFK");
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String languageCache = rs.getString("languageCache");
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String taxonUUID= rs.getString("UUID");
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String verSource = rs.getString("VerSource");
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UUID currentTaxonUuid = null;
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FaunaEuropaeaVernacularName fauEuVernacularName = new FaunaEuropaeaVernacularName();
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fauEuVernacularName.setGuid(vernameGUID);
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fauEuVernacularName.setLanguageCache(languageCache);
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fauEuVernacularName.setLanguageFk(languageFK);
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fauEuVernacularName.setVernacularName(vernacularNameString);
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fauEuVernacularName.setSource(verSource);
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fauEuVernacularName.setTaxonUuid(UUID.fromString(taxonUUID));
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currentTaxonUuid =UUID.fromString(taxonUUID);
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if (!taxonUuids.contains(currentTaxonUuid)) {
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taxonUuids.add(currentTaxonUuid);
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FaunaEuropaeaVernacularNamesTaxon fauEuVernacularNameTaxon =
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new FaunaEuropaeaVernacularNamesTaxon(currentTaxonUuid);
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fauEuVernacularNamesMap.put(currentTaxonUuid, fauEuVernacularNameTaxon);
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fauEuVernacularNameTaxon = null;
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} else {
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if (logger.isTraceEnabled()) {
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logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
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continue;
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}
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}
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fauEuVernacularNamesMap.get(currentTaxonUuid).addVernacularName(fauEuVernacularName);
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if (((i % limit) == 0 && i != 1 ) || i == count ) {
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try {
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commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
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taxonUuids = null;
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taxonList = null;
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fauEuVernacularNamesMap = null;
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} catch (Exception e) {
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logger.error("Commit of taxa and distributions failed" + e.getMessage());
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e.printStackTrace();
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}
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if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}
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}
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}
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if (taxonUuids != null){
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try {
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commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
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taxonUuids = null;
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taxonList = null;
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fauEuVernacularNamesMap = null;
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} catch (Exception e) {
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logger.error("Commit of taxa and vernacular names failed");
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logger.error(e.getMessage());
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e.printStackTrace();
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}
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}
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rs = null;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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state.setUnsuccessfull();
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}
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if(logger.isInfoEnabled()) { logger.info("End making vernacular names..."); }
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return;
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}
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}
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@Override
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protected boolean doCheck(FaunaEuropaeaImportState state) {
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// TODO Auto-generated method stub
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return false;
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}
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@Override
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protected boolean isIgnore(FaunaEuropaeaImportState state) {
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// TODO Auto-generated method stub
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return false;
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}
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private void commitTaxaAndVernacularNames(
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FaunaEuropaeaImportState state,
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Set<UUID> taxonUuids,
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Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap,
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TransactionStatus txStatus) throws Exception {
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List<TaxonBase> taxonList = prepareTaxaAndVernacularNames(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
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getTaxonService().saveOrUpdate(taxonList);
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taxonList = null;
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taxonUuids = null;
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fauEuTaxonMap = null;
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commitTransaction(txStatus);
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}
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private List<TaxonBase> prepareTaxaAndVernacularNames(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) throws Exception{
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CommonTaxonName verName = null;
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FaunaEuropaeaVernacularNamesTaxon fauEuHelperTaxon;
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UUID taxonUuid;
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TaxonDescription taxonDescription;
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Taxon taxon;
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for (TaxonBase<?> taxonBase : taxonList) {
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if (taxonBase != null) {
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if (taxonBase instanceof Taxon) {
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taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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} else {
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Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
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taxon = syn.getAcceptedTaxon();
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logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
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+ taxonBase.getClass().getSimpleName() + " using accepted Taxon for vernacular name");
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continue;
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}
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taxonDescription = TaxonDescription.NewInstance();
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addOriginalSource(taxonDescription, null, "CommonNameDefaultImport", pesiProject);
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taxon.addDescription(taxonDescription);
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taxonUuid = taxonBase.getUuid();
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fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);
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for (FaunaEuropaeaVernacularName fauEuHelperVernacularName: fauEuHelperTaxon.getVernacularNames()) {
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verName = null;
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/*
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* UUID uuid = state.getTransformer().getLanguageUuid(languageKey);
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result = (Language)getTermService().find(uuid);
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}
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if (result == null){
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result = state.getTransformer().getLanguageByKey(languageKey);
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if (result == null){
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UUID uuidLanguage;
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uuidLanguage = state.getTransformer().getLanguageUuid(languageKey);
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if (uuidLanguage == null){
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logger.warn("Language not defined: " + languageKey) ;
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}
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result = getLanguage(state, uuidLanguage, languageKey, languageKey, null);
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if (result == null){
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logger.warn("Language not defined: " + languageKey) ;
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}
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}else if (result.getId() == 0){
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// UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de");
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UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
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TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, result);
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// TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc);
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voc.addTerm(result);
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getTermService().saveOrUpdate(result);
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state.putLanguage(result);
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}
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*
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*/
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Language lang = FaunaEuropaeaTransformer.langFK2Language(fauEuHelperVernacularName.getLanguageFk());
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if (lang == null && fauEuHelperVernacularName.getLanguageFk() == 83){
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lang = Language.ENGLISH();
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fauEuHelperVernacularName.setArea("USA");
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}
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if (lang == null){
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UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
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logger.info("languageFk = " + fauEuHelperVernacularName.getLanguageFk());
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TermVocabulary<Language> voc = getVocabulary(state, TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);
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lang = Language.NewInstance("Dummy", "", "");
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voc.addTerm(lang);
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lang =(Language)getTermService().save(lang);
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FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);
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}
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// if (lang.getId() == 0){
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// UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
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// TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);
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// voc.addTerm(lang);
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// lang =(Language)getTermService().save(lang);
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// //FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);
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// }
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verName = CommonTaxonName.NewInstance(fauEuHelperVernacularName.getVernacularName(), lang);
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if (fauEuHelperVernacularName.getArea()!= null && fauEuHelperVernacularName.getArea().equals("USA")){
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verName.setArea(NamedArea.NORTH_AMERICA());
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}
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verName.setCreated(null);
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if (fauEuHelperVernacularName.getSource() != null){
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addOriginalSource(verName, null, null, sourceMap.get(fauEuHelperVernacularName.getSource()));
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}
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taxonDescription.addElement(verName);
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}
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}
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}
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return taxonList;
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}
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private void createSourceMap(FaunaEuropaeaImportState state){
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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Source source = fauEuConfig.getSource();
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TransactionStatus txStatus = null;
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String sourceSelect = "SELECT DISTINCT vernacularNames.VerSource FROM vernacularNames group by vernacularNames.VerSource";
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try {
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txStatus =startTransaction();
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ResultSet rs = source.getResultSet(sourceSelect);
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Reference sourceRef;
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String title ;
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Set<Reference> referncesToSave = new HashSet<Reference>();
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while (rs.next()) {
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sourceRef = ReferenceFactory.newGeneric();
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title = rs.getString("VerSource");
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sourceRef.setTitle(title);
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referncesToSave.add(sourceRef);
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}
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commitReferences(referncesToSave, txStatus);
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}catch (SQLException e) {
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logger.error("SQLException:" + e);
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state.setUnsuccessfull();
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}
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}
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private void commitReferences(Collection<Reference> references, TransactionStatus txStatus) {
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Map <UUID, Reference> referenceMap =getReferenceService().save(references);
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Iterator<Entry<UUID, Reference>> it = referenceMap.entrySet().iterator();
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while (it.hasNext()){
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Reference ref = it.next().getValue();
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String refID = ref.getTitle();
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sourceMap.put(refID, ref);
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}
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commitTransaction(txStatus);
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}
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}
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