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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.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.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 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.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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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.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* @author a.babadshanjan
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* @since 12.05.2009
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*/
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@Component
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public class FaunaEuropaeaDistributionImport extends FaunaEuropaeaImportBase {
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private static final long serialVersionUID = 746146902707885655L;
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
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@Override
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protected boolean doCheck(FaunaEuropaeaImportState state) {
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boolean result = true;
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logger.warn("Checking for Distributions not yet implemented");
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return result;
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}
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@Override
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protected void doInvoke(FaunaEuropaeaImportState state) {
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/*
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logger.warn("Start distribution doInvoke");
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ProfilerController.memorySnapshot();
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*/
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if (!state.getConfig().isDoOccurrence()){
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return;
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}
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int limit = state.getConfig().getLimitSave();
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UUID noDataUuid;
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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, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap = null;
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TransactionStatus txStatus = null;
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//txStatus = startTransaction();
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/*PresenceAbsenceTerm noDataStatusTerm = PresenceAbsenceTerm.NewPresenceInstance("no data", "no data", "nod");
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noDataUuid = noDataStatusTerm.getUuid();
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TermVocabulary<PresenceAbsenceTerm> voc = getVocabularyService().find(30);
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HibernateProxyHelper.deproxy(voc, OrderedTermVocabulary.class);
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//voc.addTerm(noDataStatusTerm);
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// getVocabularyService().saveOrUpdate(voc);
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getTermService().save(noDataStatusTerm);*/
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//commitTransaction(txStatus);
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// FaunaEuropaeaTransformer.setUUIDs(noDataUuid);
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logger.info("create termvoc");
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createTermVocabulary(txStatus, 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 distribution.*, Area.*, Taxon.UUID ";
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String fromClause =
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" FROM distribution INNER JOIN " +
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" Area ON distribution.dis_ara_id = Area.ara_id INNER JOIN " +
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" Taxon ON distribution.dis_tax_id = Taxon.TAX_ID ";
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String orderBy = " ORDER BY distribution.dis_tax_id";
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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 distributions..."); }
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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<>(limit);
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fauEuTaxonMap = new HashMap<>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Distribution 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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int disId = rs.getInt("dis_id");
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int occStatusId = rs.getInt("dis_present");
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int areaId = rs.getInt("ara_id");
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String areaName = rs.getString("ara_name");
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String areaCode = rs.getString("ara_code");
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int extraLimital = rs.getInt("ara_extralimital");
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UUID currentTaxonUuid = null;
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if (resultSetHasColumn(rs,"UUID")){
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currentTaxonUuid = UUID.fromString(rs.getString("UUID"));
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} else {
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currentTaxonUuid = UUID.randomUUID();
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}
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FaunaEuropaeaDistribution fauEuDistribution = new FaunaEuropaeaDistribution();
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fauEuDistribution.setDistributionId(disId);
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fauEuDistribution.setOccurrenceStatusId(occStatusId);
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fauEuDistribution.setAreaId(areaId);
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fauEuDistribution.setAreaName(areaName);
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fauEuDistribution.setAreaCode(areaCode);
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fauEuDistribution.setExtraLimital(extraLimital);
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if (!taxonUuids.contains(currentTaxonUuid)) {
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taxonUuids.add(currentTaxonUuid);
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FaunaEuropaeaDistributionTaxon fauEuDistributionTaxon =
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new FaunaEuropaeaDistributionTaxon(currentTaxonUuid);
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fauEuTaxonMap.put(currentTaxonUuid, fauEuDistributionTaxon);
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fauEuDistributionTaxon = 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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fauEuTaxonMap.get(currentTaxonUuid).addDistribution(fauEuDistribution);
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if (((i % limit) == 0 && i != 1 ) || i == count ) {
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try {
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commitTaxaAndDistribution(state, taxonUuids, fauEuTaxonMap, txStatus);
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taxonUuids = null;
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taxonList = null;
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fauEuTaxonMap = 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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commitTaxaAndDistribution(state, taxonUuids, fauEuTaxonMap, txStatus);
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taxonUuids = null;
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taxonList = null;
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fauEuTaxonMap = null;
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} catch (Exception e) {
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logger.error("Commit of taxa and distributions 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 distributions..."); }
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return;
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}
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/**
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*
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*/
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private void createTermVocabulary(TransactionStatus txStatus, FaunaEuropaeaImportState state) {
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TermVocabulary<NamedArea> faunaEuAreaVocabulary = TermVocabulary.NewInstance(TermType.NamedArea, "Areas for Fauna Europaea distribution data", "FE areas", "FE", null);
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faunaEuAreaVocabulary.setUuid(FaunaEuropaeaTransformer.uuidFauEuArea);
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NamedArea area =NamedArea.NewInstance(null, "Andorra", "AD");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("AD");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Albania", "AL");
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area.setIdInVocabulary("AL");
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area.setUuid(UUID.randomUUID());
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Austria", "AT");
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area.setIdInVocabulary("AT");
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area.setUuid(UUID.randomUUID());
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Bosnia and Herzegovina", "BA");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("BA");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Belgium", "BE");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("BE");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Bulgaria", "BG");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("BG");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Belarus", "BY");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("BY");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Switzerland", "CH");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("CH");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Cyprus", "CY");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("CY");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Czech Republic", "CZ");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("CZ");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Germany", "DE");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("DE");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance("Incl. Bornholm I.", "Danish mainland", "DK-DEN");
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area.setUuid(UUID.randomUUID());
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286
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area.setIdInVocabulary("DK-DEN");
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Faroe Is.", "DK-FOR");
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290
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area.setUuid(UUID.randomUUID());
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291
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area.setIdInVocabulary("DK-FOR");
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292
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state.putNamedArea(area);
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293
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Estonia", "EE");
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("EE");
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297
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state.putNamedArea(area);
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faunaEuAreaVocabulary.addTerm(area);
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299
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area = NamedArea.NewInstance("Incl. Mallorca I., Menorca I., and Pityuses Is.(=Ibiza I. + Formentera I.)", "Balearic Is.", "ES-BAL");
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300
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area.setUuid(UUID.randomUUID());
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301
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area.setIdInVocabulary("ES-BAL");
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302
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state.putNamedArea(area);
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303
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faunaEuAreaVocabulary.addTerm(area);
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304
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area = NamedArea.NewInstance(null, "Canary Is.", "ES-CNY");
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305
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("ES-CNY");
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state.putNamedArea(area);
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308
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faunaEuAreaVocabulary.addTerm(area);
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309
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area = NamedArea.NewInstance("Incl. Alboran I.", "Spanish mainland", "ES-SPA");
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310
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area.setUuid(UUID.randomUUID());
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311
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area.setIdInVocabulary("ES-SPA");
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312
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state.putNamedArea(area);
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313
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faunaEuAreaVocabulary.addTerm(area);
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314
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area = NamedArea.NewInstance(null, "Finland", "FI");
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315
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area.setUuid(UUID.randomUUID());
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316
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area.setIdInVocabulary("FI");
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317
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state.putNamedArea(area);
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318
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faunaEuAreaVocabulary.addTerm(area);
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319
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area = NamedArea.NewInstance(null, "Corsica", "FR-COR");
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320
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area.setUuid(UUID.randomUUID());
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321
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area.setIdInVocabulary("FR-COR");
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322
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state.putNamedArea(area);
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323
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "French mainland", "FR-FRA");
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325
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area.setUuid(UUID.randomUUID());
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326
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area.setIdInVocabulary("FR-FRA");
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state.putNamedArea(area);
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328
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faunaEuAreaVocabulary.addTerm(area);
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329
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area = NamedArea.NewInstance("Incl. Jersey, Guernsey, Alderney", "Channel Is.", "GB-CI");
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330
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area.setUuid(UUID.randomUUID());
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331
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area.setIdInVocabulary("GB-CI");
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332
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state.putNamedArea(area);
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333
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance(null, "Gibraltar", "GB-GI");
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335
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area.setUuid(UUID.randomUUID());
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area.setIdInVocabulary("GB-GI");
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337
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state.putNamedArea(area);
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338
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faunaEuAreaVocabulary.addTerm(area);
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area = NamedArea.NewInstance("Incl. Shetlands, Orkneys, Hebrides and Man Is.", "Britain I.", "GB-GRB");
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340
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area.setUuid(UUID.randomUUID());
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341
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area.setIdInVocabulary("GB-GRB");
|
|
342
|
state.putNamedArea(area);
|
|
343
|
faunaEuAreaVocabulary.addTerm(area);
|
|
344
|
area = NamedArea.NewInstance(null, "Northern Ireland", "GB-NI");
|
|
345
|
area.setUuid(UUID.randomUUID());
|
|
346
|
area.setIdInVocabulary("GB-NI");
|
|
347
|
state.putNamedArea(area);
|
|
348
|
faunaEuAreaVocabulary.addTerm(area);
|
|
349
|
area = NamedArea.NewInstance("Incl. Andípsara, Áyios Evstrátios, Foúrnoi,Ikaría, Khíos, "
|
|
350
|
+ "Lésvos, Límnos, Oinoúsa, Psará, Sámos, Skópelos Kaloyeroi and other smaller"
|
|
351
|
+ " islands","Vóreion Aiyáion (North Aegean Is.)", "GR-AEG");
|
|
352
|
area.setUuid(UUID.randomUUID());
|
|
353
|
area.setIdInVocabulary("GR-AEG");
|
|
354
|
state.putNamedArea(area);
|
|
355
|
faunaEuAreaVocabulary.addTerm(area);
|
|
356
|
area = NamedArea.NewInstance("Incl. Amorgós, Anáfi, Ánidros, Ándros, Andíparos, Denoúsa, Folégandros, "
|
|
357
|
+ "Íos, Iráklia, Káros, Kímolos, Kéa, Kýthnos, Mílos, Mýkonos, Náxos, Páros, Políaigos, Sérifos, "
|
|
358
|
+ "Sífnos, Síkinos, Sýros, Thíra, Tínos, Yiarós and other smaller islands", "Kikládes (Cyclades Is.)", "GR-CYC");
|
|
359
|
area.setUuid(UUID.randomUUID());
|
|
360
|
area.setIdInVocabulary("GR-CYC");
|
|
361
|
state.putNamedArea(area);
|
|
362
|
faunaEuAreaVocabulary.addTerm(area);
|
|
363
|
area = NamedArea.NewInstance("Incl. Alimniá, Árkoi, Astipálaia, Avgonísi, Ankathonísi, Farmakonísi, Ioinianísia,"
|
|
364
|
+ " Kálimnos, Kalolímnos, Kandelioúsa, Kárpathos, Kásos, Khálki, Khamilí, Kínaros, Kos, Léros, Levítha, "
|
|
365
|
+ "Lipsói, Meyísti, Nísiros, Ofidoúsa, Pátmos, Ródhos, Saría, Sími, Sírina, Tílos, Tría Nisiá, Yialí "
|
|
366
|
+ "and other smaller islands", "Dodekánisos (Dodecanese Is.) ", "GR-DOD");
|
|
367
|
area.setUuid(UUID.randomUUID());
|
|
368
|
area.setIdInVocabulary("GR-DOD");
|
|
369
|
state.putNamedArea(area);
|
|
370
|
faunaEuAreaVocabulary.addTerm(area);
|
|
371
|
area = NamedArea.NewInstance(" Incl. Andikíthira I., Evvia I., Ionian Is., Samothráki I., Northern Sporades Is., Thásos I.",
|
|
372
|
"Greek mainland", "GR-GRC");
|
|
373
|
area.setUuid(UUID.randomUUID());
|
|
374
|
area.setIdInVocabulary("GR-GRC");
|
|
375
|
state.putNamedArea(area);
|
|
376
|
faunaEuAreaVocabulary.addTerm(area);
|
|
377
|
area = NamedArea.NewInstance("Incl. small adjacent islands like Gávdhos. Note that Andikíthira I. although being "
|
|
378
|
+ "closer to Kriti than to mainland, belongs to a mainland province", "Kriti (Crete)", "GR-KRI");
|
|
379
|
area.setUuid(UUID.randomUUID());
|
|
380
|
area.setIdInVocabulary("GR-KRI");
|
|
381
|
state.putNamedArea(area);
|
|
382
|
faunaEuAreaVocabulary.addTerm(area);
|
|
383
|
area = NamedArea.NewInstance(null, "Croatia", "HR");
|
|
384
|
area.setUuid(UUID.randomUUID());
|
|
385
|
area.setIdInVocabulary("HR");
|
|
386
|
state.putNamedArea(area);
|
|
387
|
faunaEuAreaVocabulary.addTerm(area);
|
|
388
|
area = NamedArea.NewInstance(null, "Hungary", "HU");
|
|
389
|
area.setUuid(UUID.randomUUID());
|
|
390
|
area.setIdInVocabulary("HU");
|
|
391
|
state.putNamedArea(area);
|
|
392
|
faunaEuAreaVocabulary.addTerm(area);
|
|
393
|
area = NamedArea.NewInstance(null, "Ireland", "IE");
|
|
394
|
area.setUuid(UUID.randomUUID());
|
|
395
|
area.setIdInVocabulary("IE");
|
|
396
|
state.putNamedArea(area);
|
|
397
|
faunaEuAreaVocabulary.addTerm(area);
|
|
398
|
area = NamedArea.NewInstance(null, "Iceland", "IS");
|
|
399
|
area.setUuid(UUID.randomUUID());
|
|
400
|
area.setIdInVocabulary("IS");
|
|
401
|
state.putNamedArea(area);
|
|
402
|
faunaEuAreaVocabulary.addTerm(area);
|
|
403
|
area = NamedArea.NewInstance(null, "Italian mainland", "IT-ITA");
|
|
404
|
area.setUuid(UUID.randomUUID());
|
|
405
|
area.setIdInVocabulary("IT-ITA");
|
|
406
|
state.putNamedArea(area);
|
|
407
|
faunaEuAreaVocabulary.addTerm(area);
|
|
408
|
area = NamedArea.NewInstance(null, "Sardinia", "IT-SAR");
|
|
409
|
area.setUuid(UUID.randomUUID());
|
|
410
|
area.setIdInVocabulary("IT-SAR");
|
|
411
|
state.putNamedArea(area);
|
|
412
|
faunaEuAreaVocabulary.addTerm(area);
|
|
413
|
area = NamedArea.NewInstance(" Incl. adjacent Italian islands (Lipari Is., Ustica I., Egadi Is., "
|
|
414
|
+ "Pantelleria I., Pelagie Is.) ", "Sicily", "IT-SI");
|
|
415
|
area.setUuid(UUID.randomUUID());
|
|
416
|
area.setIdInVocabulary("IT-SI");
|
|
417
|
state.putNamedArea(area);
|
|
418
|
faunaEuAreaVocabulary.addTerm(area);
|
|
419
|
area = NamedArea.NewInstance(null, "Liechtenstein", "LI");
|
|
420
|
area.setUuid(UUID.randomUUID());
|
|
421
|
area.setIdInVocabulary("LI");
|
|
422
|
state.putNamedArea(area);
|
|
423
|
faunaEuAreaVocabulary.addTerm(area);
|
|
424
|
area = NamedArea.NewInstance(null, "Lithuania", "LT");
|
|
425
|
area.setUuid(UUID.randomUUID());
|
|
426
|
area.setIdInVocabulary("LT");
|
|
427
|
state.putNamedArea(area);
|
|
428
|
faunaEuAreaVocabulary.addTerm(area);
|
|
429
|
area = NamedArea.NewInstance(null, "Luxembourg", "LU");
|
|
430
|
area.setUuid(UUID.randomUUID());
|
|
431
|
area.setIdInVocabulary("LU");
|
|
432
|
state.putNamedArea(area);
|
|
433
|
faunaEuAreaVocabulary.addTerm(area);
|
|
434
|
area = NamedArea.NewInstance(null, "Latvia", "LV");
|
|
435
|
area.setUuid(UUID.randomUUID());
|
|
436
|
area.setIdInVocabulary("LV");
|
|
437
|
state.putNamedArea(area);
|
|
438
|
faunaEuAreaVocabulary.addTerm(area);
|
|
439
|
area = NamedArea.NewInstance(null, "Monaco", "MC");
|
|
440
|
area.setUuid(UUID.randomUUID());
|
|
441
|
area.setIdInVocabulary("MC");
|
|
442
|
state.putNamedArea(area);
|
|
443
|
faunaEuAreaVocabulary.addTerm(area);
|
|
444
|
area = NamedArea.NewInstance(null, "Moldova, Republic of", "MD");
|
|
445
|
area.setUuid(UUID.randomUUID());
|
|
446
|
area.setIdInVocabulary("MD");
|
|
447
|
state.putNamedArea(area);
|
|
448
|
faunaEuAreaVocabulary.addTerm(area);
|
|
449
|
area = NamedArea.NewInstance(null, "Macedonia, the former Yugoslav Republic of", "MK");
|
|
450
|
area.setUuid(UUID.randomUUID());
|
|
451
|
area.setIdInVocabulary("MK");
|
|
452
|
state.putNamedArea(area);
|
|
453
|
faunaEuAreaVocabulary.addTerm(area);
|
|
454
|
area = NamedArea.NewInstance(null, "Malta", "MT");
|
|
455
|
area.setUuid(UUID.randomUUID());
|
|
456
|
area.setIdInVocabulary("MT");
|
|
457
|
state.putNamedArea(area);
|
|
458
|
faunaEuAreaVocabulary.addTerm(area);
|
|
459
|
area = NamedArea.NewInstance(null, "The Netherlands", "NL");
|
|
460
|
area.setUuid(UUID.randomUUID());
|
|
461
|
area.setIdInVocabulary("NL");
|
|
462
|
state.putNamedArea(area);
|
|
463
|
faunaEuAreaVocabulary.addTerm(area);
|
|
464
|
area = NamedArea.NewInstance(null, "Norwegian mainland", "NO-NOR");
|
|
465
|
area.setUuid(UUID.randomUUID());
|
|
466
|
area.setIdInVocabulary("NO-NOR");
|
|
467
|
state.putNamedArea(area);
|
|
468
|
faunaEuAreaVocabulary.addTerm(area);
|
|
469
|
area = NamedArea.NewInstance("Incl. Bear I.", "Svalbard & Jan Mayen", "NO-SVA");
|
|
470
|
area.setUuid(UUID.randomUUID());
|
|
471
|
area.setIdInVocabulary("NO-SVA");
|
|
472
|
state.putNamedArea(area);
|
|
473
|
faunaEuAreaVocabulary.addTerm(area);
|
|
474
|
area = NamedArea.NewInstance(null, "Poland", "PL");
|
|
475
|
area.setUuid(UUID.randomUUID());
|
|
476
|
area.setIdInVocabulary("PL");
|
|
477
|
state.putNamedArea(area);
|
|
478
|
faunaEuAreaVocabulary.addTerm(area);
|
|
479
|
area = NamedArea.NewInstance(null, "Azores Is.", "PT-AZO");
|
|
480
|
area.setUuid(UUID.randomUUID());
|
|
481
|
area.setIdInVocabulary("PT-AZO");
|
|
482
|
state.putNamedArea(area);
|
|
483
|
faunaEuAreaVocabulary.addTerm(area);
|
|
484
|
area = NamedArea.NewInstance(null, "Madeira Is.", "PT-MDR");
|
|
485
|
area.setUuid(UUID.randomUUID());
|
|
486
|
area.setIdInVocabulary("PT-MDR");
|
|
487
|
state.putNamedArea(area);
|
|
488
|
faunaEuAreaVocabulary.addTerm(area);
|
|
489
|
area = NamedArea.NewInstance(null, "Portuguese mainland", "PT-POR");
|
|
490
|
area.setUuid(UUID.randomUUID());
|
|
491
|
area.setIdInVocabulary("PT-POR");
|
|
492
|
state.putNamedArea(area);
|
|
493
|
faunaEuAreaVocabulary.addTerm(area);
|
|
494
|
area = NamedArea.NewInstance(null, "Selvagens Is.", "PT-SEL");
|
|
495
|
area.setUuid(UUID.randomUUID());
|
|
496
|
area.setIdInVocabulary("PT-SEL");
|
|
497
|
state.putNamedArea(area);
|
|
498
|
faunaEuAreaVocabulary.addTerm(area);
|
|
499
|
area = NamedArea.NewInstance(null, "Romania", "RO");
|
|
500
|
area.setUuid(UUID.randomUUID());
|
|
501
|
area.setIdInVocabulary("RO");
|
|
502
|
state.putNamedArea(area);
|
|
503
|
faunaEuAreaVocabulary.addTerm(area);
|
|
504
|
area = NamedArea.NewInstance("Excl. Ushakova I. and Vize I.", "Franz Josef Land", "RU-FJL");
|
|
505
|
area.setUuid(UUID.randomUUID());
|
|
506
|
area.setIdInVocabulary("RU-FJL");
|
|
507
|
state.putNamedArea(area);
|
|
508
|
faunaEuAreaVocabulary.addTerm(area);
|
|
509
|
area = NamedArea.NewInstance(null, "Kaliningrad Region", "RU-KGD");
|
|
510
|
area.setUuid(UUID.randomUUID());
|
|
511
|
area.setIdInVocabulary("RU-KGD");
|
|
512
|
state.putNamedArea(area);
|
|
513
|
faunaEuAreaVocabulary.addTerm(area);
|
|
514
|
area = NamedArea.NewInstance(null, "Novaya Zemlya", "RU-NOZ");
|
|
515
|
area.setUuid(UUID.randomUUID());
|
|
516
|
area.setIdInVocabulary("RU-NOZ");
|
|
517
|
state.putNamedArea(area);
|
|
518
|
faunaEuAreaVocabulary.addTerm(area);
|
|
519
|
area = NamedArea.NewInstance(null, "Central European Russia", "RU-RUC");
|
|
520
|
area.setUuid(UUID.randomUUID());
|
|
521
|
area.setIdInVocabulary("RU-RUC");
|
|
522
|
state.putNamedArea(area);
|
|
523
|
faunaEuAreaVocabulary.addTerm(area);
|
|
524
|
area = NamedArea.NewInstance(null, "East European Russia", "RU-RUE");
|
|
525
|
area.setUuid(UUID.randomUUID());
|
|
526
|
area.setIdInVocabulary("RU-RUE");
|
|
527
|
state.putNamedArea(area);
|
|
528
|
|
|
529
|
faunaEuAreaVocabulary.addTerm(area);
|
|
530
|
area = NamedArea.NewInstance(null, "North European Russia", "RU-RUN");
|
|
531
|
area.setUuid(UUID.randomUUID());
|
|
532
|
area.setIdInVocabulary("RU-RUN");
|
|
533
|
state.putNamedArea(area);
|
|
534
|
faunaEuAreaVocabulary.addTerm(area);
|
|
535
|
area = NamedArea.NewInstance(null, "South European Russia", "RU-RUS");
|
|
536
|
area.setUuid(UUID.randomUUID());
|
|
537
|
area.setIdInVocabulary("RU-RUS");
|
|
538
|
state.putNamedArea(area);
|
|
539
|
faunaEuAreaVocabulary.addTerm(area);
|
|
540
|
area = NamedArea.NewInstance(null, "Northwest European Russia", "RU-RUW");
|
|
541
|
area.setUuid(UUID.randomUUID());
|
|
542
|
area.setIdInVocabulary("RU-RUW");
|
|
543
|
state.putNamedArea(area);
|
|
544
|
faunaEuAreaVocabulary.addTerm(area);
|
|
545
|
area = NamedArea.NewInstance("Incl. Gotland I.", "Sweden", "SE");
|
|
546
|
area.setUuid(UUID.randomUUID());
|
|
547
|
area.setIdInVocabulary("SE");
|
|
548
|
state.putNamedArea(area);
|
|
549
|
faunaEuAreaVocabulary.addTerm(area);
|
|
550
|
area = NamedArea.NewInstance(null, "Slovenia", "SI");
|
|
551
|
area.setUuid(UUID.randomUUID());
|
|
552
|
area.setIdInVocabulary("SI");
|
|
553
|
state.putNamedArea(area);
|
|
554
|
faunaEuAreaVocabulary.addTerm(area);
|
|
555
|
area = NamedArea.NewInstance(null, "Slovakia", "SK");
|
|
556
|
area.setUuid(UUID.randomUUID());
|
|
557
|
area.setIdInVocabulary("SK");
|
|
558
|
state.putNamedArea(area);
|
|
559
|
faunaEuAreaVocabulary.addTerm(area);
|
|
560
|
area = NamedArea.NewInstance(null, "San Marino", "SM");
|
|
561
|
area.setUuid(UUID.randomUUID());
|
|
562
|
area.setIdInVocabulary("SM");
|
|
563
|
state.putNamedArea(area);
|
|
564
|
faunaEuAreaVocabulary.addTerm(area);
|
|
565
|
area = NamedArea.NewInstance("Incl. Imroz I. - Gökçeada, but not those in the Sea of Marmara",
|
|
566
|
"European Turkey", "TR-TUE");
|
|
567
|
area.setUuid(UUID.randomUUID());
|
|
568
|
area.setIdInVocabulary("TR-TUE");
|
|
569
|
state.putNamedArea(area);
|
|
570
|
faunaEuAreaVocabulary.addTerm(area);
|
|
571
|
area = NamedArea.NewInstance(null, "Ukraine", "UA");
|
|
572
|
area.setUuid(UUID.randomUUID());
|
|
573
|
area.setIdInVocabulary("UA");
|
|
574
|
state.putNamedArea(area);
|
|
575
|
faunaEuAreaVocabulary.addTerm(area);
|
|
576
|
area = NamedArea.NewInstance(null, "Vatican City", "VA");
|
|
577
|
area.setUuid(UUID.randomUUID());
|
|
578
|
area.setIdInVocabulary("VA");
|
|
579
|
state.putNamedArea(area);
|
|
580
|
faunaEuAreaVocabulary.addTerm(area);
|
|
581
|
area = NamedArea.NewInstance("Incl. Serbia, Kosovo, Voivodina, Montenegro", "Yugoslavia", "YU");
|
|
582
|
area.setUuid(UUID.randomUUID());
|
|
583
|
area.setIdInVocabulary("YU");
|
|
584
|
state.putNamedArea(area);
|
|
585
|
faunaEuAreaVocabulary.addTerm(area);
|
|
586
|
area = NamedArea.NewInstance(null, "Afro-tropical region", "AFR");
|
|
587
|
area.setUuid(UUID.randomUUID());
|
|
588
|
area.setIdInVocabulary("AFR");
|
|
589
|
state.putNamedArea(area);
|
|
590
|
faunaEuAreaVocabulary.addTerm(area);
|
|
591
|
area = NamedArea.NewInstance(null, "Australian region", "AUS");
|
|
592
|
area.setUuid(UUID.randomUUID());
|
|
593
|
area.setIdInVocabulary("AUS");
|
|
594
|
state.putNamedArea(area);
|
|
595
|
faunaEuAreaVocabulary.addTerm(area);
|
|
596
|
area = NamedArea.NewInstance("East of the border line here defined", "East Palaearctic", "EPA");
|
|
597
|
area.setUuid(UUID.randomUUID());
|
|
598
|
area.setIdInVocabulary("EPA");
|
|
599
|
state.putNamedArea(area);
|
|
600
|
faunaEuAreaVocabulary.addTerm(area);
|
|
601
|
area = NamedArea.NewInstance("Not including Sinai Peninsula", "North Africa", "NAF");
|
|
602
|
area.setUuid(UUID.randomUUID());
|
|
603
|
area.setIdInVocabulary("NAF");
|
|
604
|
state.putNamedArea(area);
|
|
605
|
faunaEuAreaVocabulary.addTerm(area);
|
|
606
|
area = NamedArea.NewInstance(null, "Nearctic region", "NEA");
|
|
607
|
area.setUuid(UUID.randomUUID());
|
|
608
|
area.setIdInVocabulary("NEA");
|
|
609
|
state.putNamedArea(area);
|
|
610
|
faunaEuAreaVocabulary.addTerm(area);
|
|
611
|
area = NamedArea.NewInstance(null, "Neotropical region", "NEO");
|
|
612
|
area.setUuid(UUID.randomUUID());
|
|
613
|
area.setIdInVocabulary("NEO");
|
|
614
|
state.putNamedArea(area);
|
|
615
|
faunaEuAreaVocabulary.addTerm(area);
|
|
616
|
area = NamedArea.NewInstance("Asian Turkey, Caucasian Russian republics, Georgia, Armenia, Azerbaijan, "
|
|
617
|
+ "Lebanon, Syria, Israel, Jordan, Sinai Peninsula (Egypt), Arabian peninsula, Iran, Iraq",
|
|
618
|
"Near East", "NRE");
|
|
619
|
area.setUuid(UUID.randomUUID());
|
|
620
|
area.setIdInVocabulary("NRE");
|
|
621
|
state.putNamedArea(area);
|
|
622
|
faunaEuAreaVocabulary.addTerm(area);
|
|
623
|
area = NamedArea.NewInstance(null, "Oriental region", "ORR");
|
|
624
|
area.setUuid(UUID.randomUUID());
|
|
625
|
area.setIdInVocabulary("ORR");
|
|
626
|
state.putNamedArea(area);
|
|
627
|
faunaEuAreaVocabulary.addTerm(area);
|
|
628
|
if (txStatus == null){
|
|
629
|
txStatus = startTransaction();
|
|
630
|
}
|
|
631
|
//txStatus = startTransaction();
|
|
632
|
faunaEuAreaVocabulary = getVocabularyService().save(faunaEuAreaVocabulary);
|
|
633
|
logger.info("save voc");
|
|
634
|
commitTransaction(txStatus);
|
|
635
|
state.setAreaVoc(faunaEuAreaVocabulary);
|
|
636
|
}
|
|
637
|
|
|
638
|
private void commitTaxaAndDistribution(
|
|
639
|
FaunaEuropaeaImportState state,
|
|
640
|
Set<UUID> taxonUuids,
|
|
641
|
Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap,
|
|
642
|
TransactionStatus txStatus) throws Exception {
|
|
643
|
|
|
644
|
List<TaxonBase> taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
|
|
645
|
|
|
646
|
getTaxonService().save(taxonList);
|
|
647
|
taxonList = null;
|
|
648
|
taxonUuids = null;
|
|
649
|
fauEuTaxonMap = null;
|
|
650
|
commitTransaction(txStatus);
|
|
651
|
|
|
652
|
}
|
|
653
|
|
|
654
|
private List<TaxonBase> prepareTaxaAndDistribution(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) throws Exception{
|
|
655
|
|
|
656
|
Distribution newDistribution = null;
|
|
657
|
NamedArea namedArea;
|
|
658
|
PresenceAbsenceTerm presenceAbsenceStatus;
|
|
659
|
FaunaEuropaeaDistributionTaxon fauEuHelperTaxon;
|
|
660
|
UUID taxonUuid;
|
|
661
|
TaxonDescription taxonDescription;
|
|
662
|
Taxon taxon;
|
|
663
|
for (TaxonBase<?> taxonBase : taxonList) {
|
|
664
|
|
|
665
|
if (taxonBase != null) {
|
|
666
|
|
|
667
|
if (taxonBase instanceof Taxon) {
|
|
668
|
taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
669
|
} else {
|
|
670
|
logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
|
|
671
|
+ taxonBase.getClass().getSimpleName());
|
|
672
|
continue;
|
|
673
|
}
|
|
674
|
|
|
675
|
Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
|
|
676
|
if (descriptionSet.size() > 0) {
|
|
677
|
taxonDescription = descriptionSet.iterator().next();
|
|
678
|
} else {
|
|
679
|
taxonDescription = TaxonDescription.NewInstance();
|
|
680
|
taxon.addDescription(taxonDescription);
|
|
681
|
taxonDescription.setDefault(true);
|
|
682
|
//addOriginalSource(taxonDescription, null, "Default Import", state.getConfig().getSourceReference());
|
|
683
|
}
|
|
684
|
|
|
685
|
taxonUuid = taxonBase.getUuid();
|
|
686
|
fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);
|
|
687
|
|
|
688
|
for (FaunaEuropaeaDistribution fauEuHelperDistribution : fauEuHelperTaxon.getDistributions()) {
|
|
689
|
namedArea = null;
|
|
690
|
newDistribution = null;
|
|
691
|
presenceAbsenceStatus = null;
|
|
692
|
|
|
693
|
presenceAbsenceStatus = FaunaEuropaeaTransformer.occStatus2PresenceAbsence(fauEuHelperDistribution.getOccurrenceStatusId());
|
|
694
|
|
|
695
|
|
|
696
|
namedArea = state.areaId2NamedArea(fauEuHelperDistribution, state);
|
|
697
|
if (namedArea == null){
|
|
698
|
logger.warn("Area " + fauEuHelperDistribution.getAreaCode() + "not found in FE transformer");
|
|
699
|
}
|
|
700
|
if (namedArea == null){
|
|
701
|
//UUID areaUuid= FaunaEuropaeaTransformer.getUUIDByAreaAbbr(fauEuHelperDistribution.getAreaCode());
|
|
702
|
//if (areaUuid == null){
|
|
703
|
//logger.warn("Area " + fauEuHelperDistribution.getAreaCode() + "not found in FE transformer");
|
|
704
|
// }
|
|
705
|
// namedArea = getNamedArea(state, areaUuid, fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaCode(), null, null, state.getAreaVoc(), TermMatchMode.UUID_ABBREVLABEL);
|
|
706
|
// namedArea.setIdInVocabulary(fauEuHelperDistribution.getAreaCode());
|
|
707
|
// state.putNamedArea(namedArea);
|
|
708
|
}
|
|
709
|
|
|
710
|
newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
|
|
711
|
newDistribution.setCreated(null);
|
|
712
|
|
|
713
|
taxonDescription.addElement(newDistribution);
|
|
714
|
|
|
715
|
}
|
|
716
|
}
|
|
717
|
}
|
|
718
|
|
|
719
|
taxonDescription= null;
|
|
720
|
newDistribution = null;
|
|
721
|
namedArea= null;
|
|
722
|
return taxonList;
|
|
723
|
}
|
|
724
|
|
|
725
|
@Override
|
|
726
|
protected boolean isIgnore(FaunaEuropaeaImportState state){
|
|
727
|
return !state.getConfig().isDoOccurrence();
|
|
728
|
}
|
|
729
|
}
|