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// $Id$
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/**
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* Copyright (C) 2009 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.csv.redlist.out;
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import java.io.IOException;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase;
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import eu.etaxonomy.cdm.io.dwca.out.TermMapping;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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/**
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* @author a.mueller
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* @date 02.05.2011
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*
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*/
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public class CsvTaxExportTransformerRedlist extends InputTransformerBase {
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private static final Logger logger = Logger.getLogger(CsvTaxExportTransformerRedlist.class);
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// private static Map<UUID, String> nomStatusMap = new HashMap<UUID, String>();
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private static TermMapping nomStatusMapping;
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private static TermMapping rankMapping;
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private static TermMapping specimenTypeMapping;
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private static TermMapping nameTypeMapping;
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private static TermMapping sexMapping;
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private static TermMapping lifeStageMapping;
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private static TermMapping occStatusMapping;
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private static TermMapping establishmentMeansMapping;
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// public static String transformToGbifTaxonomicStatus(){
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// //TODO
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// return null;
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// }
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public static String transformToGbifNomStatus(NomenclaturalStatusType nomStatus){
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if ( nomStatus == null){
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return null;
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}else{
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if (nomStatusMapping == null){
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try {
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nomStatusMapping = new TermMapping("nomStatusToGbif.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = nomStatusMapping.getTerm(nomStatus.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("Nom. Status (" + nomStatus.getLabel() + ") could not be mapped. Use CDM status label.");
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}
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return result;
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}
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}
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// private static void initNomStatusMap() {
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// nomStatusMap.put(NomenclaturalStatusType.uuidAlternative, "alternativum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidAmbiguous, "ambigua");
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//// nomStatusMap.put(NomenclaturalStatusType.uuidCombinationIllegitimate, "");
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//// nomStatusMap.put(NomenclaturalStatusType.uuidCombinationInvalid, "");
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// nomStatusMap.put(NomenclaturalStatusType.uuidConfusum, "confusum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidConserved, "conservandum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidConservedProp, "conservandumProp");
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// //TODO Wrong at GBIF !!!: dubimum
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// nomStatusMap.put(NomenclaturalStatusType.uuidDoubtful, "dubium");
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// nomStatusMap.put(NomenclaturalStatusType.uuidIllegitimate, "illegitimum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidInvalid, "invalidum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidLegitimate, "legitimate"); //why english not latin ??
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// nomStatusMap.put(NomenclaturalStatusType.uuidNovum, "novum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidNudum, "nudum");
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// //TODO
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// nomStatusMap.put(NomenclaturalStatusType.uuidOpusUtiqueOppr, "opressa");
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// //TODO
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// nomStatusMap.put(NomenclaturalStatusType.uuidOrthographyConserved, "orthographia");
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// //TODO
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// nomStatusMap.put(NomenclaturalStatusType.uuidOrthographyConservedProp, "orthographia");
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// nomStatusMap.put(NomenclaturalStatusType.uuidProvisional, "provisorium");
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// nomStatusMap.put(NomenclaturalStatusType.uuidRejected, "rejiciendum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidRejectedProp, "rejiciendumProp");
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//// nomStatusMap.put(NomenclaturalStatusType.uuidSanctioned, "");
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//
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// nomStatusMap.put(NomenclaturalStatusType.uuidSubnudum, "rejiciendum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidSuperfluous, "superfluum");
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// nomStatusMap.put(NomenclaturalStatusType.uuidValid, "valid");
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//
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// //CDM is missing abortivum, available, combinatio, negatum, oblitum,
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// // protectum, rejiciendumUtique, rejiciendumUtiqueProp
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// }
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public static String transformToGbifRank(Rank term){
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if ( term == null){
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return null;
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}else{
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if (rankMapping == null){
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try {
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rankMapping = new TermMapping("rankToGbif.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = rankMapping.getTerm(term.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("Rank (" + term.getLabel() + ") could not be mapped. Use CDM abbreviated label instead.");
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}
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return result;
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}
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}
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public static String transformSpecimenTypeStatusToGbif(SpecimenTypeDesignationStatus status){
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if ( status == null){
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return null;
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}else{
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if (specimenTypeMapping == null){
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try {
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specimenTypeMapping = new TermMapping("specimenTypeStatusToGbif.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = specimenTypeMapping.getTerm(status.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("Specimen type status (" + status.getLabel() + ") could not be mapped. Use CDM status label.");
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}
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return result;
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}
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}
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public static String transformNameTypeStatusToGbif(NameTypeDesignationStatus status){
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if ( status == null){
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return null;
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}else{
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if (nameTypeMapping == null){
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try {
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nameTypeMapping = new TermMapping("nameTypeStatusToGbif.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = nameTypeMapping.getTerm(status.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("Name type status (" + status.getLabel() + ") could not be mapped. Use CDM status label.");
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}
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return result;
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}
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}
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public static String transformToGbifSex(DefinedTerm sex) {
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if ( sex == null){
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return null;
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}else{
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if (sexMapping == null){
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try {
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sexMapping = new TermMapping("sexToGbif.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = sexMapping.getTerm(sex.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("Sex (" + sex.getLabel() + ") could not be mapped. Use CDM status label.");
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}
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return result;
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}
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}
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public static String transformToGbifLifeStage(DefinedTerm stage) {
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if ( stage == null){
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return null;
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}else{
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if (lifeStageMapping == null){
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try {
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lifeStageMapping = new TermMapping("lifeStageToGbif.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = lifeStageMapping.getTerm(stage.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("Life stage (" + stage.getLabel() + ") could not be mapped. Use CDM status label.");
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}
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return result;
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}
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}
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public static String transformToGbifOccStatus(PresenceAbsenceTerm status) {
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if ( status == null){
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return null;
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}else{
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if (occStatusMapping == null){
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try {
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occStatusMapping = new TermMapping("presenceTermToGbifOccurrenceStatus.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = occStatusMapping.getTerm(status.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("PresenceAbsence term (" + status.getLabel() + ") could not be mapped to GBIF occurrence status. Use CDM status label.");
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}
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return result;
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}
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}
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public static String transformToGbifEstablishmentMeans(PresenceAbsenceTerm status) {
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if ( status == null){
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return null;
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}else{
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if (establishmentMeansMapping == null){
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try {
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establishmentMeansMapping = new TermMapping("presenceTermToGbifEstablishmentMeans.tsv");
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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String result = establishmentMeansMapping.getTerm(status.getUuid());
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if (StringUtils.isBlank(result)){
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logger.info("PresenceAbsence term (" + status.getLabel() + ") could not be mapped to GBIF establishment means. Use CDM status label.");
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}
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return result;
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}
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}
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}
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