app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoConabioCommonNamesImport.java

   1 /**
   2 * Copyright (C) 2016 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.mexico;
  10
  11 import eu.etaxonomy.cdm.common.URI;
  12 import java.util.HashMap;
  13 import java.util.Map;
  14 import java.util.Set;
  15 import java.util.UUID;
  16
  17 import org.apache.commons.lang3.StringUtils;
  18 import org.apache.log4j.Logger;
  19 import org.springframework.stereotype.Component;
  20
  21 import eu.etaxonomy.cdm.model.common.Language;
  22 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  23 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  24 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  25 import eu.etaxonomy.cdm.model.reference.Reference;
  26 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  27 import eu.etaxonomy.cdm.model.taxon.Taxon;
  28 import eu.etaxonomy.cdm.model.term.TermType;
  29 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  30
  31 /**
  32  * @author a.mueller
  33  * @since 16.06.2016
  34  *
  35  */
  36 @Component
  37 public class MexicoConabioCommonNamesImport<CONFIG extends MexicoConabioImportConfigurator>
  38             extends SimpleExcelTaxonImport<CONFIG>{
  39
  40     private static final long serialVersionUID = 3579868489510261569L;
  41
  42     private static final Logger logger = Logger.getLogger(MexicoConabioCommonNamesImport.class);
  43
  44     private TermVocabulary<Language> languagesVoc;
  45     private Map<String, Language> languagesMap = new HashMap<>();
  46
  47     private Map<String, Taxon> taxonIdMap;
  48
  49
  50     @Override
  51     protected String getWorksheetName(CONFIG config) {
  52         return "NombresComunes";
  53     }
  54
  55     @Override
  56     protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
  57         initLanguageVocabulary(state);
  58         initTaxa();
  59
  60         String line = state.getCurrentLine() + ": ";
  61         Map<String, String> record = state.getOriginalRecord();
  62
  63         String idCat = getValue(record, "IdCAT");
  64         Taxon taxon = taxonIdMap.get(idCat);
  65         if (taxon == null){
  66             logger.warn(line + "Taxon could not be found: " + idCat);
  67         }else{
  68             TaxonDescription desc = getTaxonDescription(taxon);
  69             String nomComunStr = getValue(record, "NomComun");
  70             String langStr = getValueNd(record, "Lengua");
  71             Language language = languagesMap.get(langStr);
  72             if (language == null && langStr != null){
  73                 addNewLanguage(state, langStr);
  74             }
  75             logger.warn("Common names for the same taxon using the same common name but differing in source are currently not yet deduplicated. Needs to be fixed for next import");
  76
  77             String refStr = getValue(record, "ReferenciasNombreComun");
  78             CommonTaxonName commonName = CommonTaxonName.NewInstance(nomComunStr,
  79                     language, null);
  80             desc.addElement(commonName);
  81
  82             Reference ref = getReference(state, refStr);
  83             if (ref != null){
  84                 commonName.addSource(OriginalSourceType.PrimaryTaxonomicSource,
  85                         null, null, ref, null);
  86             }
  87
  88
  89             getTaxonService().save(taxon);
  90         }
  91     }
  92
  93     private Language addNewLanguage(SimpleExcelTaxonImportState<CONFIG> state, String langStr) {
  94         UUID uuid = getNewLanguageUuid(langStr);
  95         if (uuid != null){
  96             Language newLanguage = addLanguage(state, langStr, uuid);
  97             getTermService().saveOrUpdate(newLanguage);
  98             logger.warn("New language added: " + langStr + "("+ uuid + ")");
  99             return newLanguage;
 100         }else{
 101             logger.warn("Language not recognized: " + langStr);
 102             return null;
 103         }
 104     }
 105
 106     private UUID getNewLanguageUuid(String langStr) {
 107         if (langStr.equals("Mixteco")){return MexicoConabioTransformer.uuidMixteco;}
 108         else if (langStr.equals("Náhuatl-Español")){return MexicoConabioTransformer.uuidNahuatlEspanol;}
 109         else if (langStr.equals("Español-Náhuatl")){return MexicoConabioTransformer.uuidEspanolNahuatl;}
 110         else if (langStr.equals("Tzotzil")){return MexicoConabioTransformer.uuidTzotzil;}
 111         else if (langStr.equals("Tetzal")){return MexicoConabioTransformer.uuidTetzal;}
 112         else if (langStr.equals("Tzeltal")){return MexicoConabioTransformer.uuidTzeltal;}
 113         else if (langStr.equals("Mazateco")){return MexicoConabioTransformer.uuidMazateco;}
 114         else if (langStr.equals("Tepehua")){return MexicoConabioTransformer.uuidTepehua;}
 115
 116         else if (langStr.equals("Cuicateco")){return MexicoConabioTransformer.uuidCuicateco;}
 117         else if (langStr.equals("Zoque")){return MexicoConabioTransformer.uuidZoque;}
 118         else if (langStr.equals("Tepehuano")){return MexicoConabioTransformer.uuidTepehuano;}
 119         else if (langStr.equals("Popoloca")){return MexicoConabioTransformer.uuidPopoloca;}
 120         else if (langStr.equals("Tojolabal")){return MexicoConabioTransformer.uuidTojolabal;}
 121
 122         else if (langStr.equals("Mayo")){return MexicoConabioTransformer.uuidMayo;}
 123         else if (langStr.equals("Huichol")){return MexicoConabioTransformer.uuidHuichol;}
 124         else if (langStr.equals("Cora")){return MexicoConabioTransformer.uuidCora;}
 125         else if (langStr.equals("Seri")){return MexicoConabioTransformer.uuidSeri;}
 126
 127
 128
 129
 130         return null;
 131     }
 132
 133     private void initTaxa() {
 134         if (taxonIdMap == null){
 135             Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet();
 136             taxonIdMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class,
 137                     existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE);
 138         }
 139     }
 140
 141     /**
 142      * @param state
 143      */
 144     @SuppressWarnings("unchecked")
 145     private void initLanguageVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {
 146         if (languagesVoc == null){
 147             languagesVoc = this.getVocabularyService().find(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
 148             if (languagesVoc == null){
 149                 createLanguagesVoc(state);
 150             }else{
 151                 fillLanguageMap();
 152             }
 153         }
 154     }
 155
 156     private void fillLanguageMap() {
 157         for (Language language: languagesVoc.getTerms()){
 158             String label = language.getLabel();
 159             languagesMap.put(label, language);
 160         }
 161     }
 162
 163     private void createLanguagesVoc(SimpleExcelTaxonImportState<CONFIG> state) {
 164         URI termSourceUri = null;
 165         String label = "Mexican States";
 166         String description = "Mexican languages as used by the CONABIO Rubiaceae database";
 167         languagesVoc = TermVocabulary.NewInstance(TermType.Language, Language.class,
 168                 description, label, null, termSourceUri);
 169         languagesVoc.setUuid(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
 170
 171         addLanguage(state, "Chontal", MexicoConabioTransformer.uuidChontal);
 172         addLanguage(state, "Chinanteco", MexicoConabioTransformer.uuidChinanteco);
 173         addLanguage(state, "Chiapaneca", MexicoConabioTransformer.uuidChiapaneca);
 174         addLanguage(state, "Huasteco", MexicoConabioTransformer.uuidHuasteco);
 175         addLanguage(state, "Español-Maya", MexicoConabioTransformer.uuidEspanol_Maya);
 176         addLanguage(state, "Guarijío", MexicoConabioTransformer.uuidGuarijio);
 177         addLanguage(state, "Huave", MexicoConabioTransformer.uuidHuave);
 178         addLanguage(state, "Español", MexicoConabioTransformer.uuidEspanol);
 179         addLanguage(state, "Maya", MexicoConabioTransformer.uuidMaya);
 180         addLanguage(state, "Lacandón", MexicoConabioTransformer.uuidLacandon);
 181         addLanguage(state, "Inglés", MexicoConabioTransformer.uuidIngles);
 182         addLanguage(state, "Itzmal", MexicoConabioTransformer.uuidItzmal);
 183         addLanguage(state, "Náhuatl", MexicoConabioTransformer.uuidNahuatl);
 184         addLanguage(state, "Tarahumara", MexicoConabioTransformer.uuidTarahumara);
 185         addLanguage(state, "Otomí", MexicoConabioTransformer.uuidOtomi);
 186         addLanguage(state, "Mixe", MexicoConabioTransformer.uuidMixe);
 187         addLanguage(state, "Tseltal", MexicoConabioTransformer.uuidTseltal);
 188         addLanguage(state, "Zapoteco", MexicoConabioTransformer.uuidZapoteco);
 189         addLanguage(state, "Totonaco", MexicoConabioTransformer.uuidTotonaco);
 190         addLanguage(state, "Tarasco", MexicoConabioTransformer.uuidTarasco);
 191
 192         this.getVocabularyService().save(languagesVoc);
 193
 194         return;
 195     }
 196
 197     private Language addLanguage(SimpleExcelTaxonImportState<CONFIG> state, String label, UUID uuid) {
 198         String abbrev = null;
 199         Language language = Language.NewInstance(
 200                 label, label, abbrev);
 201         language.setUuid(uuid);
 202         languagesVoc.addTerm(language);
 203         languagesMap.put(label, language);
 204         return language;
 205     }
 206
 207     private Reference getReference(SimpleExcelTaxonImportState<CONFIG> state, String refStr) {
 208         if (StringUtils.isBlank(refStr)){
 209             return null;
 210         }
 211         Reference ref = state.getReference(refStr);
 212         if (ref == null){
 213             ref = ReferenceFactory.newBook();
 214             ref.setTitleCache(refStr, true);
 215             state.putReference(refStr, ref);
 216         }
 217         return ref;
 218     }
 219
 220     /**
 221      * @param taxon
 222      * @return
 223      */
 224     private TaxonDescription getTaxonDescription(Taxon taxon) {
 225         if (!taxon.getDescriptions().isEmpty()){
 226             return taxon.getDescriptions().iterator().next();
 227         }else{
 228             TaxonDescription desc = TaxonDescription.NewInstance(taxon);
 229             return desc;
 230         }
 231     }
 232
 233     private String getValueNd(Map<String, String> record, String string) {
 234         String value = getValue(record, string);
 235         if ("ND".equals(value)){
 236             return null;
 237         }else{
 238             return value;
 239         }
 240     }
 241
 242     @Override
 243     protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
 244         return ! state.getConfig().isDoCommonNames();
 245     }
 246
 247 }