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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.berlinModel.in;
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import java.net.URI;
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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.Map;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelAreaImportValidator;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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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.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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@Component
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public class BerlinModelAreaImport extends BerlinModelImportBase {
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private static final long serialVersionUID = -2810052908318645219L;
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private static final Logger logger = Logger.getLogger(BerlinModelAreaImport.class);
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public static final String NAMESPACE = "emArea";
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private static final String pluralString = "areas";
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private static final String dbTableName = "emArea"; //??
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public BerlinModelAreaImport(){
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super(dbTableName, pluralString);
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}
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@Override
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protected String getIdQuery(BerlinModelImportState state) {
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String result = " SELECT AreaId FROM " + getTableName();
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// if (StringUtils.isNotBlank(state.getConfig().getOccurrenceFilter())){
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// result += " WHERE " + state.getConfig().getOccurrenceFilter();
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// }
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return result;
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}
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery =
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" SELECT * "
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+ " FROM emArea a "
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+ " WHERE (a.AreaId IN (" + ID_LIST_TOKEN + ") )"
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// + " ORDER BY PTaxon.RIdentifier"
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;
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return strQuery;
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}
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private Map<Integer, NamedArea> euroMedAreas = new HashMap<>();
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private TermVocabulary<NamedArea> createEuroMedAreas(BerlinModelImportState state) throws SQLException {
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logger.warn("Start creating E+M areas");
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Source source = state.getConfig().getSource();
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Reference sourceReference = state.getConfig().getSourceReference();
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TransactionStatus txStatus = this.startTransaction();
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sourceReference = getSourceReference(sourceReference);
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TermVocabulary<NamedArea> euroMedAreasVoc = makeEmptyEuroMedVocabulary();
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MarkerType eurMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurArea, "eur", "eur Area", "eur", getEuroMedMarkerTypeVoc());
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MarkerType euroMedAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurMedArea, "EuroMedArea", "EuroMedArea", "EuroMedArea", getEuroMedMarkerTypeVoc());
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ExtensionType isoCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidIsoCode, "IsoCode", "IsoCode", "iso");
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ExtensionType tdwgCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidTdwgAreaCode, "TDWG code", "TDWG Area code", "tdwg");
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ExtensionType mclCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidMclCode, "MCL code", "MedCheckList code", "mcl");
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NamedAreaLevel areaLevelTop = getNamedAreaLevel(state, BerlinModelTransformer.uuidEuroMedAreaLevelTop, "Euro+Med top area level", "Euro+Med top area level. This level is only to be used for the area representing the complete Euro+Med area", "e+m top", null);
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NamedAreaLevel areaLevelEm1 = getNamedAreaLevel(state, BerlinModelTransformer.uuidEuroMedAreaLevelFirst, "Euro+Med 1. area level", "Euro+Med 1. area level", "e+m 1.", null);
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NamedAreaLevel areaLevelEm2 = getNamedAreaLevel(state, BerlinModelTransformer.uuidEuroMedAreaLevelSecond, "Euro+Med 2. area level", "Euro+Med 2. area level", "Euro+Med 1. area level", null);
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String sql = "SELECT * , CASE WHEN EMCode = 'EM' THEN 'a' ELSE 'b' END as isEM " +
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" FROM emArea " +
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" ORDER BY isEM, EMCode";
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ResultSet rs = source.getResultSet(sql);
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NamedArea euroMedArea = null;
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NamedArea lastLevel1Area = null;
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//euroMedArea (EMCode = 'EM')
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rs.next();
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euroMedArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType, isoCodeExtType, tdwgCodeExtType, mclCodeExtType,
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areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel1Area);
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euroMedAreasVoc.addTerm(euroMedArea);
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//all other areas
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while (rs.next()){
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NamedArea newArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType,
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isoCodeExtType, tdwgCodeExtType, mclCodeExtType,
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areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel1Area);
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if (newArea != null){
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euroMedAreasVoc.addTerm(newArea);
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if (newArea.getPartOf().equals(euroMedArea)){
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lastLevel1Area = newArea;
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}
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}
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}
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emAreaFinetuning(euroMedAreasVoc, areaLevelEm2);
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markAreasAsHidden(state, euroMedAreasVoc);
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getVocabularyService().saveOrUpdate(euroMedAreasVoc);
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try {
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commitTransaction(txStatus);
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} catch (Exception e) {
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e.printStackTrace();
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logger.error("An exception occurred when trying to commit E+M Areas");
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}
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logger.warn("Created E+M areas");
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return euroMedAreasVoc;
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}
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/**
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* @param areaLevelEm2
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* @param euroMedAreas2
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*/
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private void emAreaFinetuning(TermVocabulary<NamedArea> euroMedAreas, NamedAreaLevel areaLevelEm2) {
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//CZ
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NamedArea oldArea = euroMedAreas.getTermByIdInvocabulary("Cz");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Cs"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sk"), areaLevelEm2);
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//Ju
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oldArea = euroMedAreas.getTermByIdInvocabulary("Ju");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("BH"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Cg"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Ct"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Mk"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sl"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sr"), areaLevelEm2);
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//IJ
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oldArea = euroMedAreas.getTermByIdInvocabulary("IJ");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Ir"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Jo"), areaLevelEm2);
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//LS
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oldArea = euroMedAreas.getTermByIdInvocabulary("LS");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Le"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sy"), areaLevelEm2);
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}
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//5.Mark areas to be hidden #3979 .5
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private void markAreasAsHidden(BerlinModelImportState state, TermVocabulary<NamedArea> euroMedAreasVoc) {
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try {
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MarkerType hiddenAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidHiddenArea,
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"Hidden Area","Used to hide distributions for the named areas in publications", null, getEuroMedMarkerTypeVoc());
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//Add hidden area marker to Rs(C) and Rs(N)
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
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} catch (Exception e) {
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e.printStackTrace();
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logger.error("Exception in markAreasAsHidden: " + e.getMessage());
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}
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}
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private void hideArea(TermVocabulary<NamedArea> euroMedAreasVoc, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
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for (NamedArea namedArea : euroMedAreasVoc){
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if (namedArea.getUuid().equals(areaUuid)){
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namedArea.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
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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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* @param oldArea
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* @param namedArea
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* @param areaLevelEm2
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*/
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private void makeSubterm(NamedArea oldArea, NamedArea namedArea, NamedAreaLevel areaLevelEm2) {
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namedArea.setLevel(areaLevelEm2);
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namedArea.setPartOf(oldArea);
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}
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/**
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* @param eurMarkerType
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* @param euroMedAreaMarkerType
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* @param isoCodeExtType
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* @param tdwgCodeExtType
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* @param mclCodeExtType
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* @param rs
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* @param areaLevelEm2
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* @param areaLevelEm1
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* @param areaLevelTop
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* @throws SQLException
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*/
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private NamedArea makeSingleEuroMedArea(ResultSet rs, MarkerType eurMarkerType,
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MarkerType euroMedAreaMarkerType, ExtensionType isoCodeExtType,
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ExtensionType tdwgCodeExtType, ExtensionType mclCodeExtType,
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NamedAreaLevel areaLevelTop, NamedAreaLevel areaLevelEm1, NamedAreaLevel areaLevelEm2,
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Reference sourceReference, NamedArea euroMedArea, NamedArea level1Area) throws SQLException {
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Integer areaId = rs.getInt("AreaId");
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String emCode = nullSafeTrim(rs.getString("EMCode"));
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String isoCode = nullSafeTrim(rs.getString("ISOCode"));
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String tdwgCode = nullSafeTrim(rs.getString("TDWGCode"));
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String unit = nullSafeTrim(rs.getString("Unit"));
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// ,[Status]
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// ,[OutputOrder]
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boolean eurMarker = rs.getBoolean("eur");
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boolean euroMedAreaMarker = rs.getBoolean("EuroMedArea");
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String notes = nullSafeTrim(rs.getString("Notes"));
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String mclCode = nullSafeTrim(rs.getString("MCLCode"));
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String geoSearch = nullSafeTrim(rs.getString("NameForGeoSearch"));
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if (isBlank(emCode)){
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emCode = unit;
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}
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//uuid
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UUID uuid = BerlinModelTransformer.getEMAreaUuid(emCode);
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NamedArea area = (NamedArea)getTermService().find(uuid);
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if (area == null){
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//label
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area = NamedArea.NewInstance(geoSearch, unit, emCode);
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if (uuid != null){
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area.setUuid(uuid);
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}else{
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if (areaId == 211 || areaId == 213){ //Additional Azores and Canary Is. area are merged into primary area, see also area.addSource part below
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return null;
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}
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logger.warn("Uuid for emCode could not be defined: " + emCode);
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}
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}
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//code
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area.setIdInVocabulary(emCode);
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//notes
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if (StringUtils.isNotEmpty(notes)){
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area.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT()));
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}
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//markers
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area.addMarker(Marker.NewInstance(eurMarkerType, eurMarker));
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area.addMarker(Marker.NewInstance(euroMedAreaMarkerType, euroMedAreaMarker));
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//extensions
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if (isNotBlank(isoCode)){
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area.addExtension(isoCode, isoCodeExtType);
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}
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if (isNotBlank(tdwgCode)){
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area.addExtension(tdwgCode, tdwgCodeExtType);
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}
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if (isNotBlank(mclCode)){
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area.addExtension(mclCode, mclCodeExtType);
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}
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//type
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area.setType(NamedAreaType.ADMINISTRATION_AREA());
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//source
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area.addSource(OriginalSourceType.Import, String.valueOf(areaId), NAMESPACE, sourceReference, null);
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//add duplicate area ids for canary
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if (areaId == 624){ //Canary Is.
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area.addSource(OriginalSourceType.Import, String.valueOf(213), NAMESPACE, sourceReference, null);
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}
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if (areaId == 210){//Azores
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area.addSource(OriginalSourceType.Import, String.valueOf(211), NAMESPACE, sourceReference, null);
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}
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//parent
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if (euroMedArea != null){
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if (emCode.contains("(")){
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area.setPartOf(level1Area);
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area.setLevel(areaLevelEm2);
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}else{
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area.setPartOf(euroMedArea);
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area.setLevel(areaLevelEm1);
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}
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}else{
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area.setLevel(areaLevelTop);
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}
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this.euroMedAreas.put(areaId, area);
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//save
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getTermService().saveOrUpdate(area);
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return area;
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}
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private String nullSafeTrim(String string) {
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if (string == null){
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return null;
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}else{
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return string.trim();
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}
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}
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/**
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*
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*/
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private TermVocabulary<NamedArea> makeEmptyEuroMedVocabulary() {
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TermType type = TermType.NamedArea;
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String description = "Euro+Med area vocabulary";
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String label = "E+M areas";
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String abbrev = null;
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URI termSourceUri = null;
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OrderedTermVocabulary<NamedArea> result = OrderedTermVocabulary.NewInstance(type, description, label, abbrev, termSourceUri);
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353
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result.setUuid(BerlinModelTransformer.uuidVocEuroMedAreas);
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getVocabularyService().save(result);
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return result;
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
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TermVocabulary<?> voc = getVocabularyService().find(BerlinModelTransformer.uuidVocEuroMedAreas);
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if (voc == null){
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try {
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createEuroMedAreas(state);
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} catch (SQLException e) {
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logger.warn("Exception when creating areas: " + e.getMessage());
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e.printStackTrace();
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}
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}
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return true;
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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return result;
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}
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@Override
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protected boolean doCheck(BerlinModelImportState state){
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IOValidator<BerlinModelImportState> validator = new BerlinModelAreaImportValidator();
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return validator.validate(state);
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}
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387
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@Override
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protected boolean isIgnore(BerlinModelImportState state){
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if (! (state.getConfig().isDoOccurrence() || state.getConfig().isDoCommonNames())){
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return true;
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}else{
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if (!this.checkSqlServerColumnExists(state.getConfig().getSource(), "emArea", "AreaId")){
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394
|
logger.error("emArea table or AreaId column do not exist. Must ignore area import");
|
395
|
return true;
|
396
|
}else{
|
397
|
return false;
|
398
|
}
|
399
|
}
|
400
|
}
|
401
|
|
402
|
}
|