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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.greece;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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 14.12.2016
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*/
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public abstract class FloraHellenicaImportBase<CONFIG extends FloraHellenicaImportConfigurator>
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extends SimpleExcelTaxonImport<CONFIG>{
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private static final long serialVersionUID = 2593130403213346396L;
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private static final Logger logger = Logger.getLogger(FloraHellenicaImportBase.class);
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private Map<UUID, Taxon> acceptedTaxonMap = new HashMap<>();
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private Reference sourceReference;
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private Reference secReference;
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private Reference secReference2;
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protected 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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desc.setDefault(true);
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return desc;
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}
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}
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protected Reference getSourceCitation(SimpleExcelTaxonImportState<CONFIG> state) {
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if (this.sourceReference == null){
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this.sourceReference = getPersistentReference(state.getConfig().getSourceReference());
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}
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return this.sourceReference;
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}
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protected Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state) {
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if (this.secReference == null){
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this.secReference = getPersistentReference(state.getConfig().getSecReference());
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}
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return this.secReference;
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}
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protected Reference getSecReference2(SimpleExcelTaxonImportState<CONFIG> state) {
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if (this.secReference2 == null){
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this.secReference2 = getPersistentReference(state.getConfig().getSecReference2());
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}
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return this.secReference2;
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}
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private Reference getPersistentReference(Reference reference) {
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Reference result = getReferenceService().find(reference.getUuid());
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if (result == null){
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result = reference;
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}
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return result;
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}
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protected Taxon getAcceptedTaxon(Map<String, String> record,
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SimpleExcelTaxonImportState<CONFIG> state, String key) {
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String accStr = getValue(record, key);
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if (accStr == null){
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return null;
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}
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accStr = accStr.trim();
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Taxon accTaxon = state.getTaxon(accStr);
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if (accTaxon == null){
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String message = state.getCurrentLine()+ ": Accepted taxon could not be found: " + accStr;
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logger.warn(message);
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return null;
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}else{
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initAcceptedTaxonMap();
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// accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());
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accTaxon = acceptedTaxonMap.get(accTaxon.getUuid());
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}
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return accTaxon;
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}
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private void initAcceptedTaxonMap() {
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if (acceptedTaxonMap.isEmpty()){
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List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null);
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for (Taxon taxon : list){
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acceptedTaxonMap.put(taxon.getUuid(), taxon);
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}
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}
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}
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/**
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* @param record
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* @param state
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* @return
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*/
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protected Taxon getHigherTaxon(Map<String, String> record,
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SimpleExcelTaxonImportState<CONFIG> state, String key) {
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String accStr = getValue(record, key);
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if (accStr == null){
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return null;
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}
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accStr = accStr.trim();
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Taxon accTaxon = state.getHigherTaxon(accStr);
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if (accTaxon == null){
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String message = state.getCurrentLine()+ ": Higher taxon could not be found: " + accStr;
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logger.info(message); //not critical
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return null;
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}else{
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initAcceptedTaxonMap();
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// accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());
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accTaxon = acceptedTaxonMap.get(accTaxon.getUuid());
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}
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return accTaxon;
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}
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protected TaxonName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,
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String famStr) {
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TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
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famStr = famStr.substring(0,1).toUpperCase() + famStr.substring(1).toLowerCase();
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name.setGenusOrUninomial(famStr);
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name.addSource(makeOriginalSource(state));
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return name;
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}
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protected TaxonName replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, TaxonName name) {
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TaxonName result = state.getDeduplicationHelper().getExistingName(name);
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state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(result);
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return result;
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}
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@Override
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protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {
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return IdentifiableSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, getSourceCitation(state));
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}
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}
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