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                 logger.warn("Language not found: " + langStr);
  74             }
  75
  76             String refStr = getValue(record, "ReferenciasNombreComun");
  77             CommonTaxonName commonName = CommonTaxonName.NewInstance(nomComunStr,
  78                     language, null);
  79             desc.addElement(commonName);
  80
  81             Reference ref = getReference(state, refStr);
  82             if (ref != null){
  83                 commonName.addSource(OriginalSourceType.PrimaryTaxonomicSource,
  84                         null, null, ref, null);
  85             }
  86
  87
  88             getTaxonService().save(taxon);
  89         }
  90     }
  91
  92     private void initTaxa() {
  93         if (taxonIdMap == null){
  94             Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet();
  95             taxonIdMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class,
  96                     existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE);
  97         }
  98     }
  99
 100     /**
 101      * @param state
 102      */
 103     @SuppressWarnings("unchecked")
 104     private void initLanguageVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {
 105         if (languagesVoc == null){
 106             languagesVoc = this.getVocabularyService().find(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
 107             if (languagesVoc == null){
 108                 createLanguagesVoc(state);
 109             }
 110         }
 111     }
 112
 113     /**
 114      * @param state
 115      * @return
 116      */
 117     private void createLanguagesVoc(SimpleExcelTaxonImportState<CONFIG> state) {
 118         URI termSourceUri = null;
 119         String label = "Mexican States";
 120         String description = "Mexican languages as used by the CONABIO Rubiaceae database";
 121         languagesVoc = TermVocabulary.NewInstance(TermType.Language, Language.class,
 122                 description, label, null, termSourceUri);
 123         languagesVoc.setUuid(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
 124
 125         addLanguage(state, "Chontal", MexicoConabioTransformer.uuidChontal);
 126         addLanguage(state, "Chinanteco", MexicoConabioTransformer.uuidChinanteco);
 127         addLanguage(state, "Chiapaneca", MexicoConabioTransformer.uuidChiapaneca);
 128         addLanguage(state, "Huasteco", MexicoConabioTransformer.uuidHuasteco);
 129         addLanguage(state, "Español-Maya", MexicoConabioTransformer.uuidEspanol_Maya);
 130         addLanguage(state, "Guarijío", MexicoConabioTransformer.uuidGuarijio);
 131         addLanguage(state, "Huave", MexicoConabioTransformer.uuidHuave);
 132         addLanguage(state, "Español", MexicoConabioTransformer.uuidEspanol);
 133         addLanguage(state, "Maya", MexicoConabioTransformer.uuidMaya);
 134         addLanguage(state, "Lacandón", MexicoConabioTransformer.uuidLacandon);
 135         addLanguage(state, "Inglés", MexicoConabioTransformer.uuidIngles);
 136         addLanguage(state, "Itzmal", MexicoConabioTransformer.uuidItzmal);
 137         addLanguage(state, "Náhuatl", MexicoConabioTransformer.uuidNahuatl);
 138         addLanguage(state, "Tarahumara", MexicoConabioTransformer.uuidTarahumara);
 139         addLanguage(state, "Otomí", MexicoConabioTransformer.uuidOtomi);
 140         addLanguage(state, "Mixe", MexicoConabioTransformer.uuidMixe);
 141         addLanguage(state, "Tseltal", MexicoConabioTransformer.uuidTseltal);
 142         addLanguage(state, "Zapoteco", MexicoConabioTransformer.uuidZapoteco);
 143         addLanguage(state, "Totonaco", MexicoConabioTransformer.uuidTotonaco);
 144         addLanguage(state, "Tarasco", MexicoConabioTransformer.uuidTarasco);
 145
 146         this.getVocabularyService().save(languagesVoc);
 147
 148         return;
 149     }
 150
 151     /**
 152      * @param state
 153      * @param string
 154      * @param uuidaguascalientes
 155      */
 156     private void addLanguage(SimpleExcelTaxonImportState<CONFIG> state, String label, UUID uuid) {
 157         String abbrev = null;
 158         Language language = Language.NewInstance(
 159                 label, label, abbrev);
 160         language.setUuid(uuid);
 161         languagesVoc.addTerm(language);
 162         languagesMap.put(label, language);
 163     }
 164
 165     /**
 166      * @param state
 167      * @param refStr
 168      * @return
 169      */
 170     private Reference getReference(SimpleExcelTaxonImportState<CONFIG> state, String refStr) {
 171         if (StringUtils.isNoneBlank(refStr)){
 172             return null;
 173         }
 174         Reference ref = state.getReference(refStr);
 175         if (ref == null){
 176             ref = ReferenceFactory.newBook();
 177             ref.setTitleCache(refStr, true);
 178             state.putReference(refStr, ref);
 179         }
 180         return ref;
 181     }
 182
 183     /**
 184      * @param taxon
 185      * @return
 186      */
 187     private TaxonDescription getTaxonDescription(Taxon taxon) {
 188         if (!taxon.getDescriptions().isEmpty()){
 189             return taxon.getDescriptions().iterator().next();
 190         }else{
 191             TaxonDescription desc = TaxonDescription.NewInstance(taxon);
 192             return desc;
 193         }
 194     }
 195
 196     private String getValueNd(Map<String, String> record, String string) {
 197         String value = getValue(record, string);
 198         if ("ND".equals(value)){
 199             return null;
 200         }else{
 201             return value;
 202         }
 203     }
 204
 205     @Override
 206     protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
 207         return ! state.getConfig().isDoCommonNames();
 208     }
 209
 210 }