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/**
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* Copyright (C) 2016 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.mexico;
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import java.net.URI;
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import java.util.HashMap;
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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.commons.lang3.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;
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import eu.etaxonomy.cdm.ext.geo.GeoServiceAreaAnnotatedMapping;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.model.common.Language;
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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.Representation;
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import eu.etaxonomy.cdm.model.common.TermType;
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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.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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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* @author a.mueller
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* @since 16.06.2016
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*
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*/
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@Component
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public class MexicoConabioDistributionImport<CONFIG extends MexicoConabioImportConfigurator>
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extends SimpleExcelTaxonImport<CONFIG> {
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private static final long serialVersionUID = -1733208053395372094L;
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private static final Logger logger = Logger.getLogger(MexicoConabioDistributionImport.class);
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private OrderedTermVocabulary<NamedArea> stateAreasVoc;
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private NamedArea mexico;
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private Map<String, Taxon> taxonIdMap;
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@Override
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protected String getWorksheetName() {
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return "DistribucionEstatal";
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}
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@SuppressWarnings("unchecked")
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private void initTaxa() {
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if (taxonIdMap == null){
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Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet();
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taxonIdMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(Taxon.class,
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existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE);
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}
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}
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
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initAreaVocabulary(state);
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initTaxa();
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String line = state.getCurrentLine() + ": ";
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HashMap<String, String> record = state.getOriginalRecord();
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String idCat = getValue(record, "IdCAT");
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Taxon taxon = taxonIdMap.get(idCat);
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if (taxon == null){
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logger.warn(line + "Taxon could not be found: " + idCat);
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}else{
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TaxonDescription desc = getTaxonDescription(taxon);
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String distrStatusStr = getValue(record, "TipoDistribucion");
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try {
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if (distrStatusStr != null){
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PresenceAbsenceTerm mexicanDistributionStatus = state.getTransformer().getPresenceTermByKey(distrStatusStr);
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if (mexicanDistributionStatus == null){
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UUID statusUuid = state.getTransformer().getPresenceTermUuid(distrStatusStr);
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mexicanDistributionStatus = getPresenceTerm(state, statusUuid,
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distrStatusStr, distrStatusStr, null, false);
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}
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if (mexicanDistributionStatus != null){
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Distribution mexicanDistribution = Distribution.NewInstance(mexico, mexicanDistributionStatus);
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desc.addElement(mexicanDistribution);
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String refStr = getValue(record, "ReferenciaTipoDistribucion");
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Reference ref = getReference(state, refStr);
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if (ref != null){
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mexicanDistribution.addSource(OriginalSourceType.PrimaryTaxonomicSource,
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null, null, ref, null);
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}
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}
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}
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} catch (UndefinedTransformerMethodException e) {}
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handleDistribution(state, desc, "AGUASCALIENTES", MexicoConabioTransformer.uuidAguascalientes, line);
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handleDistribution(state, desc, "BAJA CALIFORNIA", MexicoConabioTransformer.uuidBaja_california, line);
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handleDistribution(state, desc, "BAJA CALIFORNIA SUR", MexicoConabioTransformer.uuidBaja_california_sur, line);
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handleDistribution(state, desc, "CAMPECHE", MexicoConabioTransformer.uuidCampeche, line);
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handleDistribution(state, desc, "COAHUILA DE ZARAGOZA", MexicoConabioTransformer.uuidCoahuila_de_zaragoza, line);
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handleDistribution(state, desc, "COLIMA", MexicoConabioTransformer.uuidColima, line);
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handleDistribution(state, desc, "CHIAPAS", MexicoConabioTransformer.uuidChiapas, line);
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handleDistribution(state, desc, "CHIHUAHUA", MexicoConabioTransformer.uuidChihuahua, line);
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handleDistribution(state, desc, "DISTRITO FEDERAL", MexicoConabioTransformer.uuidDistrito_federal, line);
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handleDistribution(state, desc, "DURANGO", MexicoConabioTransformer.uuidDurango, line);
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handleDistribution(state, desc, "GUANAJUATO", MexicoConabioTransformer.uuidGuanajuato, line);
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handleDistribution(state, desc, "GUERRERO", MexicoConabioTransformer.uuidGuerrero, line);
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handleDistribution(state, desc, "HIDALGO", MexicoConabioTransformer.uuidHidalgo, line);
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handleDistribution(state, desc, "JALISCO", MexicoConabioTransformer.uuidJalisco, line);
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handleDistribution(state, desc, "MEXICO", MexicoConabioTransformer.uuidMexico, line);
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handleDistribution(state, desc, "MICHOACAN DE OCAMPO", MexicoConabioTransformer.uuidMichoacan_de_ocampo, line);
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handleDistribution(state, desc, "MORELOS", MexicoConabioTransformer.uuidMorelos, line);
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handleDistribution(state, desc, "NAYARIT", MexicoConabioTransformer.uuidNayarit, line);
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handleDistribution(state, desc, "NUEVO LEON", MexicoConabioTransformer.uuidNuevo_leon, line);
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handleDistribution(state, desc, "OAXACA", MexicoConabioTransformer.uuidOaxaca, line);
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handleDistribution(state, desc, "PUEBLA", MexicoConabioTransformer.uuidPuebla, line);
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handleDistribution(state, desc, "QUERETARO DE ARTEAGA", MexicoConabioTransformer.uuidQueretaro_de_arteaga, line);
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handleDistribution(state, desc, "QUINTANA ROO", MexicoConabioTransformer.uuidQuintana_roo, line);
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handleDistribution(state, desc, "SAN LUIS POTOSI", MexicoConabioTransformer.uuidSan_luis_potosi, line);
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handleDistribution(state, desc, "SINALOA", MexicoConabioTransformer.uuidSinaloa, line);
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handleDistribution(state, desc, "SONORA", MexicoConabioTransformer.uuidSonora, line);
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handleDistribution(state, desc, "TABASCO", MexicoConabioTransformer.uuidTabasco, line);
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handleDistribution(state, desc, "TAMAULIPAS", MexicoConabioTransformer.uuidTamaulipas, line);
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handleDistribution(state, desc, "TLAXCALA", MexicoConabioTransformer.uuidTlaxcala, line);
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handleDistribution(state, desc, "VERACRUZ DE IGNACIO DE LA LLAVE", MexicoConabioTransformer.uuidVeracruz_de_ignacio_de_la_llave, line);
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handleDistribution(state, desc, "YUCATAN", MexicoConabioTransformer.uuidYucatan, line);
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handleDistribution(state, desc, "ZACATECAS", MexicoConabioTransformer.uuidZacatecas, line);
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getTaxonService().save(taxon);
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}
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}
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/**
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* @param state
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* @param refStr
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* @return
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*/
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private Reference getReference(SimpleExcelTaxonImportState<CONFIG> state, String refStr) {
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if (StringUtils.isNoneBlank(refStr)){
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return null;
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}
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Reference ref = state.getReference(refStr);
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if (ref == null){
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ref = ReferenceFactory.newBook();
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ref.setTitleCache(refStr, true);
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state.putReference(refStr, ref);
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}
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return ref;
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}
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/**
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* @param desc
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* @param string
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* @param uuidUserDefinedAnnotationTypeVocabulary
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*/
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private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state, TaxonDescription desc, String key,
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UUID uuid, String line) {
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HashMap<String, String> record = state.getOriginalRecord();
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String value = getValue(record, key);
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if ("1".equals(value)){
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NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);
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Distribution dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT());
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desc.addElement(dist);
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}else if (value != null){
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logger.warn(line + "Unrecognized distribution status '" + value + "' for " + key);
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}
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}
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/**
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* @param taxon
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* @return
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*/
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private TaxonDescription getTaxonDescription(Taxon taxon) {
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if (!taxon.getDescriptions().isEmpty()){
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return taxon.getDescriptions().iterator().next();
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}else{
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TaxonDescription desc = TaxonDescription.NewInstance(taxon);
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return desc;
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}
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}
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/**
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* @param state
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*/
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@SuppressWarnings("unchecked")
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private void initAreaVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {
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if (stateAreasVoc == null){
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stateAreasVoc = (OrderedTermVocabulary<NamedArea>)this.getVocabularyService().find(MexicoConabioTransformer.uuidMexicanStatesVoc);
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if (stateAreasVoc == null){
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createStateAreasVoc(state);
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}
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}
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}
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/**
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* @param state
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* @return
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*/
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@SuppressWarnings("unchecked")
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private void createStateAreasVoc(SimpleExcelTaxonImportState<CONFIG> state) {
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//voc
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URI termSourceUri = null;
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String label = "Mexican States";
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String description = "Mexican States as used by the CONABIO Rubiaceae database";
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stateAreasVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea,
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description, label, null, termSourceUri);
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stateAreasVoc.setUuid(MexicoConabioTransformer.uuidMexicanStatesVoc);
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Representation rep = Representation.NewInstance("Estados Méxicanos", "Estados Méxicanos", null, Language.SPANISH_CASTILIAN());
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stateAreasVoc.addRepresentation(rep);
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//mexico country
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String mexicoLabel = "Mexico (Country)";
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mexico = NamedArea.NewInstance(
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mexicoLabel, mexicoLabel, null);
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mexico.setUuid(MexicoConabioTransformer.uuidMexicoCountry);
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stateAreasVoc.addTerm(mexico);
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addMapping(mexico, "mex_adm0", "iso", "MEX");
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//Example with almost all areas is Chiococca alba
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addArea(state, "Aguascalientes", MexicoConabioTransformer.uuidAguascalientes);
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addArea(state, "Baja California", MexicoConabioTransformer.uuidBaja_california);
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addArea(state, "Baja California Sur", MexicoConabioTransformer.uuidBaja_california_sur);
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addArea(state, "Campeche", MexicoConabioTransformer.uuidCampeche);
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addArea(state, "Coahuila de Zaragoza", MexicoConabioTransformer.uuidCoahuila_de_zaragoza, "Coahuila");
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addArea(state, "Colima", MexicoConabioTransformer.uuidColima);
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addArea(state, "Chiapas", MexicoConabioTransformer.uuidChiapas);
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addArea(state, "Chihuahua", MexicoConabioTransformer.uuidChihuahua);
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addArea(state, "Distrito Federal", MexicoConabioTransformer.uuidDistrito_federal);
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addArea(state, "Durango", MexicoConabioTransformer.uuidDurango);
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addArea(state, "Guanajuato", MexicoConabioTransformer.uuidGuanajuato);
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addArea(state, "Guerrero", MexicoConabioTransformer.uuidGuerrero);
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addArea(state, "Hidalgo", MexicoConabioTransformer.uuidHidalgo);
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addArea(state, "Jalisco", MexicoConabioTransformer.uuidJalisco);
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//id_1
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addArea(state, "México", MexicoConabioTransformer.uuidMexico, null, 15);
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//id_1
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addArea(state, "Michoacan de Ocampo", MexicoConabioTransformer.uuidMichoacan_de_ocampo, "Michoacán", 16);
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addArea(state, "Morelos", MexicoConabioTransformer.uuidMorelos);
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addArea(state, "Nayarit", MexicoConabioTransformer.uuidNayarit);
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//gibt beim mapping vielleicht Probleme wg. des Accents
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//id_1
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addArea(state, "Nuevo Leon", MexicoConabioTransformer.uuidNuevo_leon, "Nuevo León", 19);
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addArea(state, "Oaxaca", MexicoConabioTransformer.uuidOaxaca);
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addArea(state, "Puebla", MexicoConabioTransformer.uuidPuebla);
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//id_1
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addArea(state, "Queretaro de Arteaga", MexicoConabioTransformer.uuidQueretaro_de_arteaga, "Querétaro", 22);
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addArea(state, "Quintana Roo", MexicoConabioTransformer.uuidQuintana_roo);
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//id_1
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addArea(state, "San Luis Potosí", MexicoConabioTransformer.uuidSan_luis_potosi,null ,24);
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addArea(state, "Sinaloa", MexicoConabioTransformer.uuidSinaloa);
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addArea(state, "Sonora", MexicoConabioTransformer.uuidSonora);
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addArea(state, "Tabasco", MexicoConabioTransformer.uuidTabasco);
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addArea(state, "Tamaulipas", MexicoConabioTransformer.uuidTamaulipas);
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addArea(state, "Tlaxcala", MexicoConabioTransformer.uuidTlaxcala);
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addArea(state, "Veracruz de Ignacio de la Llave", MexicoConabioTransformer.uuidVeracruz_de_ignacio_de_la_llave, "Veracruz");
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//??
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addArea(state, "Yucatán", MexicoConabioTransformer.uuidYucatan, null, 31);
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addArea(state, "Zacatecas", MexicoConabioTransformer.uuidZacatecas);
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this.getVocabularyService().save(stateAreasVoc);
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return;
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}
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private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid) {
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addArea(state, areaLabel, uuid, areaLabel); //short cut if label and mapping label are equal
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}
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private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid, String mappingLabel) {
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addArea(state, areaLabel, uuid, mappingLabel, null); //short cut if label and mapping label are equal
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}
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/**
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* @param state
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* @param string
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* @param uuidaguascalientes
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*/
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private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid, String mappingLabel, Integer id1) {
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String abbrev = null;
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NamedArea newArea = NamedArea.NewInstance(
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areaLabel, areaLabel, abbrev);
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newArea.setUuid(uuid);
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newArea.setPartOf(mexico);
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newArea.setLevel(NamedAreaLevel.STATE());
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newArea.setType(NamedAreaType.ADMINISTRATION_AREA());
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stateAreasVoc.addTerm(newArea);
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if (id1 != null){
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addMapping(newArea, "mex_adm1", "id_1", String.valueOf(id1));
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}else if (mappingLabel != null){
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addMapping(newArea, "mex_adm1", "name_1", mappingLabel);
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}
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}
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private void addMapping(NamedArea area, String mapping_layer, String mapping_field, String abbrev) {
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GeoServiceAreaAnnotatedMapping mapping = (GeoServiceAreaAnnotatedMapping)this.getBean("geoServiceAreaAnnotatedMapping");
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GeoServiceArea geoServiceArea = new GeoServiceArea();
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geoServiceArea.add(mapping_layer, mapping_field, abbrev);
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mapping.set(area, geoServiceArea);
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}
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@Override
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protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
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return ! state.getConfig().isDoDistributions();
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}
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}
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