cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExportTransformer.java

   1 /**
   2 * Copyright (C) 2009 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.io.dwca.out;
  10
  11 import java.io.IOException;
  12
  13 import org.apache.commons.lang.StringUtils;
  14 import org.apache.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase;
  17 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  18 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  19 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  20 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  21 import eu.etaxonomy.cdm.model.name.Rank;
  22 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  23
  24 /**
  25  * @author a.mueller
  26  * @date 02.05.2011
  27  *
  28  */
  29 public class DwcaTaxExportTransformer extends InputTransformerBase {
  30         private static final Logger logger = Logger.getLogger(DwcaTaxExportTransformer.class);
  31
  32 //      private static Map<UUID, String> nomStatusMap = new HashMap<UUID, String>();
  33         private static TermMapping nomStatusMapping;
  34         private static TermMapping rankMapping;
  35         private static TermMapping specimenTypeMapping;
  36         private static TermMapping nameTypeMapping;
  37         private static TermMapping sexMapping;
  38         private static TermMapping lifeStageMapping;
  39         private static TermMapping occStatusMapping;
  40         private static TermMapping establishmentMeansMapping;
  41
  42
  43 //      public static String transformToGbifTaxonomicStatus(){
  44 //              //TODO
  45 //              return null;
  46 //      }
  47
  48         public static String transformToGbifNomStatus(NomenclaturalStatusType nomStatus){
  49                 if ( nomStatus == null){
  50                         return null;
  51                 }else{
  52                         if (nomStatusMapping == null){
  53                                 try {
  54                                         nomStatusMapping = new TermMapping("nomStatusToGbif.tsv");
  55                                 } catch (IOException e) {
  56                                         throw new RuntimeException(e);
  57                                 }
  58                         }
  59                         String result = nomStatusMapping.getTerm(nomStatus.getUuid());
  60                         if (StringUtils.isBlank(result)){
  61                                 logger.info("Nom. Status (" + nomStatus.getLabel() + ") could not be mapped. Use CDM status label.");
  62                         }
  63                         return result;
  64                 }
  65         }
  66
  67 //      private static void initNomStatusMap() {
  68 //              nomStatusMap.put(NomenclaturalStatusType.uuidAlternative, "alternativum");
  69 //              nomStatusMap.put(NomenclaturalStatusType.uuidAmbiguous, "ambigua");
  70 ////            nomStatusMap.put(NomenclaturalStatusType.uuidCombinationIllegitimate, "");
  71 ////            nomStatusMap.put(NomenclaturalStatusType.uuidCombinationInvalid, "");
  72 //              nomStatusMap.put(NomenclaturalStatusType.uuidConfusum, "confusum");
  73 //              nomStatusMap.put(NomenclaturalStatusType.uuidConserved, "conservandum");
  74 //              nomStatusMap.put(NomenclaturalStatusType.uuidConservedProp, "conservandumProp");
  75 //              //TODO Wrong at GBIF !!!: dubimum
  76 //              nomStatusMap.put(NomenclaturalStatusType.uuidDoubtful, "dubium");
  77 //              nomStatusMap.put(NomenclaturalStatusType.uuidIllegitimate, "illegitimum");
  78 //              nomStatusMap.put(NomenclaturalStatusType.uuidInvalid, "invalidum");
  79 //              nomStatusMap.put(NomenclaturalStatusType.uuidLegitimate, "legitimate");  //why english not latin ??
  80 //              nomStatusMap.put(NomenclaturalStatusType.uuidNovum, "novum");
  81 //              nomStatusMap.put(NomenclaturalStatusType.uuidNudum, "nudum");
  82 //              //TODO
  83 //              nomStatusMap.put(NomenclaturalStatusType.uuidOpusUtiqueOppr, "opressa");
  84 //              //TODO
  85 //              nomStatusMap.put(NomenclaturalStatusType.uuidOrthographyConserved, "orthographia");
  86 //              //TODO
  87 //              nomStatusMap.put(NomenclaturalStatusType.uuidOrthographyConservedProp, "orthographia");
  88 //              nomStatusMap.put(NomenclaturalStatusType.uuidProvisional, "provisorium");
  89 //              nomStatusMap.put(NomenclaturalStatusType.uuidRejected, "rejiciendum");
  90 //              nomStatusMap.put(NomenclaturalStatusType.uuidRejectedProp, "rejiciendumProp");
  91 ////            nomStatusMap.put(NomenclaturalStatusType.uuidSanctioned, "");
  92 //
  93 //              nomStatusMap.put(NomenclaturalStatusType.uuidSubnudum, "rejiciendum");
  94 //              nomStatusMap.put(NomenclaturalStatusType.uuidSuperfluous, "superfluum");
  95 //              nomStatusMap.put(NomenclaturalStatusType.uuidValid, "valid");
  96 //
  97 //              //CDM is missing abortivum, available, combinatio, negatum, oblitum,
  98 //              //               protectum, rejiciendumUtique, rejiciendumUtiqueProp
  99 //      }
 100
 101         public static String transformToGbifRank(Rank term){
 102                 if ( term == null){
 103                         return null;
 104                 }else{
 105                         if (rankMapping == null){
 106                                 try {
 107                                         rankMapping = new TermMapping("rankToGbif.tsv");
 108                                 } catch (IOException e) {
 109                                         throw new RuntimeException(e);
 110                                 }
 111                         }
 112                         String result = rankMapping.getTerm(term.getUuid());
 113                         if (StringUtils.isBlank(result)){
 114                                 logger.info("Rank (" + term.getLabel() + ") could not be mapped. Use CDM abbreviated label instead.");
 115                         }
 116                         return result;
 117                 }
 118         }
 119
 120         public static String transformSpecimenTypeStatusToGbif(SpecimenTypeDesignationStatus status){
 121                 if ( status == null){
 122                         return null;
 123                 }else{
 124                         if (specimenTypeMapping == null){
 125                                 try {
 126                                         specimenTypeMapping = new TermMapping("specimenTypeStatusToGbif.tsv");
 127                                 } catch (IOException e) {
 128                                         throw new RuntimeException(e);
 129                                 }
 130                         }
 131                         String result = specimenTypeMapping.getTerm(status.getUuid());
 132                         if (StringUtils.isBlank(result)){
 133                                 logger.info("Specimen type status (" + status.getLabel() + ") could not be mapped. Use CDM status label.");
 134                         }
 135                         return result;
 136                 }
 137         }
 138
 139
 140         public static String transformNameTypeStatusToGbif(NameTypeDesignationStatus status){
 141                 if ( status == null){
 142                         return null;
 143                 }else{
 144                         if (nameTypeMapping == null){
 145                                 try {
 146                                         nameTypeMapping = new TermMapping("nameTypeStatusToGbif.tsv");
 147                                 } catch (IOException e) {
 148                                         throw new RuntimeException(e);
 149                                 }
 150                         }
 151                         String result = nameTypeMapping.getTerm(status.getUuid());
 152                         if (StringUtils.isBlank(result)){
 153                                 logger.info("Name type status (" + status.getLabel() + ") could not be mapped. Use CDM status label.");
 154                         }
 155                         return result;
 156                 }
 157         }
 158
 159         public static String transformToGbifSex(DefinedTerm sex) {
 160                 if ( sex == null){
 161                         return null;
 162                 }else{
 163                         if (sexMapping == null){
 164                                 try {
 165                                         sexMapping = new TermMapping("sexToGbif.tsv");
 166                                 } catch (IOException e) {
 167                                         throw new RuntimeException(e);
 168                                 }
 169                         }
 170                         String result = sexMapping.getTerm(sex.getUuid());
 171                         if (StringUtils.isBlank(result)){
 172                                 logger.info("Sex (" + sex.getLabel() + ") could not be mapped. Use CDM status label.");
 173                         }
 174                         return result;
 175                 }
 176         }
 177
 178         public static String transformToGbifLifeStage(DefinedTerm stage) {
 179                 if ( stage == null){
 180                         return null;
 181                 }else{
 182                         if (lifeStageMapping == null){
 183                                 try {
 184                                         lifeStageMapping = new TermMapping("lifeStageToGbif.tsv");
 185                                 } catch (IOException e) {
 186                                         throw new RuntimeException(e);
 187                                 }
 188                         }
 189                         String result = lifeStageMapping.getTerm(stage.getUuid());
 190                         if (StringUtils.isBlank(result)){
 191                                 logger.info("Life stage (" + stage.getLabel() + ") could not be mapped. Use CDM status label.");
 192                         }
 193                         return result;
 194                 }
 195         }
 196
 197         public static String transformToGbifOccStatus(PresenceAbsenceTerm status) {
 198                 if ( status == null){
 199                         return null;
 200                 }else{
 201                         if (occStatusMapping == null){
 202                                 try {
 203                                         occStatusMapping = new TermMapping("presenceTermToGbifOccurrenceStatus.tsv");
 204                                 } catch (IOException e) {
 205                                         throw new RuntimeException(e);
 206                                 }
 207                         }
 208                         String result = occStatusMapping.getTerm(status.getUuid());
 209                         if (StringUtils.isBlank(result)){
 210                                 logger.info("PresenceAbsence term (" + status.getLabel() + ") could not be mapped to GBIF occurrence status. Use CDM status label.");
 211                         }
 212                         return result;
 213                 }
 214         }
 215
 216         public static String transformToGbifEstablishmentMeans(PresenceAbsenceTerm status) {
 217                 if ( status == null){
 218                         return null;
 219                 }else{
 220                         if (establishmentMeansMapping == null){
 221                                 try {
 222                                         establishmentMeansMapping = new TermMapping("presenceTermToGbifEstablishmentMeans.tsv");
 223                                 } catch (IOException e) {
 224                                         throw new RuntimeException(e);
 225                                 }
 226                         }
 227                         String result = establishmentMeansMapping.getTerm(status.getUuid());
 228                         if (StringUtils.isBlank(result)){
 229                                 logger.info("PresenceAbsence term (" + status.getLabel() + ") could not be mapped to GBIF establishment means. Use CDM status label.");
 230                         }
 231                         return result;
 232                 }
 233         }
 234
 235 }