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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.redlist.germanSL;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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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.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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/**
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* @author a.mueller
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* @since 25.11.2016
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*
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*/
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@Component
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public class GermanSLTaxonRelationImport extends GermanSLTaxonImport {
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private static final long serialVersionUID = 3381597141845204995L;
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private static final Logger logger = Logger.getLogger(GermanSLTaxonRelationImport.class);
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public static final String TAXON_NAMESPACE = "1.3.4";
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@Override
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protected String getWorksheetName(GermanSLImportConfigurator config) {
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return "1.3.4";
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}
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private Classification classification;
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private Set<TaxonNode> nodesToSave = new HashSet<>();
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private int count = 0;
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
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count++;
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Map<String, String> record = state.getOriginalRecord();
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String line = state.getCurrentLine() + ": ";
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String parentStr = getValue(record, GermanSLTaxonImport.AGG);
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String acceptedStr = getValue(record, GermanSLTaxonImport.VALID_NR);
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String idStr = getValue(record, GermanSLTaxonImport.SPECIES_NR);
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String statusStr = getValue(record, GermanSLTaxonImport.SYNONYM);
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NameResult nameResult = makeName (line, record, state);
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Classification classification = getClassification(state);
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TaxonBase<?> taxonBase = GermanSLTaxonImport.taxonIdMap.get(idStr);
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Taxon parent;
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TaxonNode taxonNode = null;
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if (isAccepted(statusStr, nameResult)){
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TaxonBase<?> parentTmp = GermanSLTaxonImport.taxonIdMap.get(parentStr);
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if (parentTmp == null){
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logger.warn(line + "Parent is missing: "+ parentStr);
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}else if (parentTmp.isInstanceOf(Synonym.class)){
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logger.warn(line + "Parent is not of type Taxon");
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}else{
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parent = (Taxon)parentTmp;
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Taxon taxon = (Taxon)taxonBase;
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Reference relRef = null; //TODO
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if ("0".equals(idStr)){
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taxonNode = classification.addChildTaxon(taxon, relRef, null);
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}else{
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taxonNode = classification.addParentChild(parent, taxon, relRef, null);
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}
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}
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} else {
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TaxonBase<?> parentTmp = GermanSLTaxonImport.taxonIdMap.get(acceptedStr);
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if (parentTmp == null){
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logger.warn(line + "Accepted taxon is missing: " + acceptedStr);
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}else if (parentTmp.isInstanceOf(Synonym.class)){
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logger.warn(line + "Accepted taxon is not of type Taxon");
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}else{
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parent = (Taxon)parentTmp;
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Synonym synonym = (Synonym)taxonBase;
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parent.addSynonym(synonym, SynonymType.SYNONYM_OF());
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}
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}
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if (taxonNode != null){
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nodesToSave.add(taxonNode);
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}
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if ((count % 1) == 0){
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count = 0;
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getTaxonNodeService().saveOrUpdate(nodesToSave);
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nodesToSave = new HashSet<>();
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}
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}
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boolean needsFinalSave = true;
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/**
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* {@inheritDoc}
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*/
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@Override
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protected void secondPass(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
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if (needsFinalSave){
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getTaxonNodeService().saveOrUpdate(nodesToSave);
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needsFinalSave = false;
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}
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}
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/**
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* @return
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*/
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private Classification getClassification(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
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if (classification == null){
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GermanSLImportConfigurator config = state.getConfig();
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classification = Classification.NewInstance(config.getClassificationName());
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classification.setUuid(config.getClassificationUuid());
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classification.setReference(config.getSecReference());
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getClassificationService().save(classification);
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}
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return classification;
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}
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@Override
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protected boolean isIgnore(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
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return ! state.getConfig().isDoTaxa();
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}
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}
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