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

   1 /**
   2 * Copyright (C) 2007 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 java.sql.ResultSet;
  12 import java.sql.SQLException;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.common.URI;
  24 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  25 import eu.etaxonomy.cdm.model.common.CdmBase;
  26 import eu.etaxonomy.cdm.model.common.Language;
  27 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  28 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  29 import eu.etaxonomy.cdm.model.location.NamedArea;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33 import eu.etaxonomy.cdm.model.term.TermType;
  34 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  35
  36 /**
  37  * @author a.mueller
  38  * @since 08.02.2022
  39  */
  40 @Component
  41 public class MexicoEfloraCommonNameImport extends MexicoEfloraImportBase {
  42
  43     private static final long serialVersionUID = 8616047381536678637L;
  44     private static final Logger logger = Logger.getLogger(MexicoEfloraCommonNameImport.class);
  45
  46         protected static final String NAMESPACE = "CommonNames";
  47
  48         private static final String pluralString = "common names";
  49         private static final String dbTableName = "Eflora_NombresComunes4CDM";
  50
  51         private Map<String,Language> languageMap = new HashMap<>();
  52
  53         public MexicoEfloraCommonNameImport(){
  54                 super(dbTableName, pluralString);
  55         }
  56
  57         @Override
  58         protected String getIdQuery(MexicoEfloraImportState state) {
  59                 String sql = " SELECT IdCombinado "
  60                         + " FROM " + dbTableName
  61                         + " ORDER BY IdCat, IdCombinado ";
  62                 return sql;
  63         }
  64
  65         @Override
  66         protected String getRecordQuery(MexicoEfloraImportConfigurator config) {
  67                 String sqlSelect = " SELECT cn.*, t.uuid taxonUuid ";
  68                 String sqlFrom = " FROM " + dbTableName + " cn "
  69                                 + " LEFT JOIN " + MexicoEfloraTaxonImport.dbTableName + " t ON cn.IdCAT = t.IdCAT ";
  70                 String sqlWhere = " WHERE ( IdCombinado IN (" + ID_LIST_TOKEN + ") )";
  71
  72                 String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere ;
  73                 return strRecordQuery;
  74         }
  75
  76         @Override
  77     protected void doInvoke(MexicoEfloraImportState state) {
  78         createLanguageMap(state);
  79         super.doInvoke(state);
  80     }
  81
  82     private void createLanguageMap(MexicoEfloraImportState state) {
  83         TermVocabulary<Language> voc = createLanguagesVoc(state);
  84
  85         String sql = "SELECT * FROM cv4_Controlled_vocabulary_for_languages ";
  86         ResultSet rs = state.getConfig().getSource().getResultSet(sql);
  87         try {
  88             while (rs.next()) {
  89                 String lang = rs.getString("Lengua");
  90                 Language language = Language.NewInstance(lang, lang, null, Language.SPANISH_CASTILIAN());
  91                 voc.addTerm(language);
  92                 getTermService().save(language);  //not sure if necessary
  93                 languageMap.put(lang, language);
  94             }
  95         } catch (SQLException e) {
  96             e.printStackTrace();
  97         }
  98     }
  99
 100     private TermVocabulary<Language> createLanguagesVoc(MexicoEfloraImportState state) {
 101         URI termSourceUri = null;
 102         String label = "Mexican Languages";
 103         String description = "Mexican languages as used by the CONABIO database";
 104         TermVocabulary<Language> languagesVoc = TermVocabulary.NewInstance(TermType.Language, Language.class,
 105                 description, label, null, termSourceUri);
 106         languagesVoc.setUuid(MexicoConabioTransformer.uuidMexicanLanguagesVoc);
 107         this.getVocabularyService().save(languagesVoc);
 108
 109         return languagesVoc;
 110     }
 111
 112     @Override
 113         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, MexicoEfloraImportState state) {
 114
 115             boolean success = true ;
 116
 117             @SuppressWarnings("rawtypes")
 118         Set<TaxonBase> taxaToSave = new HashSet<>();
 119
 120             @SuppressWarnings("unchecked")
 121         Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(MexicoEfloraTaxonImport.NAMESPACE);
 122
 123                 ResultSet rs = partitioner.getResultSet();
 124                 try{
 125                         while (rs.next()){
 126
 127                         //      if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
 128
 129                                 //create TaxonName element
 130                                 String idCombi = rs.getString("IdCombinado");
 131 //                          String idNomComun = rs.getString("IdNomComun");
 132                             String taxonUuid = rs.getString("taxonUuid");
 133
 134                             String nomComunStr = rs.getString("NomComun");
 135                             String lenguaStr = rs.getString("Lengua");
 136                             //TODO handle country in
 137 //                          String paisStr = rs.getString("Pais");
 138 //                          String estadoStr = rs.getString("Estado");
 139                             int idRegion = rs.getInt("IdRegion");
 140
 141                             try {
 142                                 TaxonBase<?> taxonBase = taxonMap.get(taxonUuid);
 143                                 Taxon taxon;
 144                                 if (taxonBase.isInstanceOf(Taxon.class)) {
 145                                     taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 146                                 }else {
 147                                     logger.warn(idCombi + ": Taxon is not accepted: " + taxonUuid);
 148                                     continue;
 149                                 }
 150
 151                                 Language language = getLanguage(state, lenguaStr);
 152                                 NamedArea area = getArea(state, idRegion);
 153                                 CommonTaxonName commonName = CommonTaxonName.NewInstance(nomComunStr,
 154                                         language, area);
 155                                 //TODO
 156                                 Reference ref = null;
 157                                 TaxonDescription description = this.getTaxonDescription(taxon, ref,
 158                                         false, true);
 159                                 description.addElement(commonName);
 160
 161                                 state.getCommonNameMap().put(idCombi, commonName);
 162
 163                                         partitioner.startDoSave();
 164                                         taxaToSave.add(taxonBase);
 165                                 } catch (Exception e) {
 166                                         logger.warn("An exception (" +e.getMessage()+") occurred when trying to create common name for id " + idCombi + ".");
 167                                         success = false;
 168                                 }
 169                         }
 170                 } catch (Exception e) {
 171                         logger.error("SQLException:" +  e);
 172                         return false;
 173                 }
 174
 175                 getTaxonService().save(taxaToSave);
 176                 return success;
 177         }
 178
 179     private NamedArea getArea(MexicoEfloraImportState state, Integer idRegion) {
 180         NamedArea area = state.getAreaMap().get(idRegion);
 181         if (idRegion != null && area == null) {
 182             logger.warn("Area not found: " + idRegion);
 183         }
 184         return area;
 185     }
 186
 187     private Language getLanguage(MexicoEfloraImportState state, String lenguaStr) {
 188         Language language = languageMap.get(lenguaStr);
 189         if (isNotBlank(lenguaStr) && language == null) {
 190             logger.warn("Language not found: " + lenguaStr);
 191         }
 192         return language;
 193     }
 194
 195     @Override
 196         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, MexicoEfloraImportState state) {
 197
 198         String nameSpace;
 199                 Set<String> idSet;
 200                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 201
 202                 try{
 203             Set<UUID> taxonIdSet = new HashSet<>();
 204                         Set<String> referenceIdSet = new HashSet<>();
 205                         while (rs.next()){
 206                 handleForeignUuidKey(rs, taxonIdSet, "taxonUuid");
 207 //                              handleForeignKey(rs, referenceIdSet, "PTRefFk");
 208                         }
 209
 210             //taxon map
 211             nameSpace = MexicoEfloraTaxonImport.NAMESPACE;
 212             @SuppressWarnings("rawtypes")
 213             Map<String, TaxonBase> taxonMap = new HashMap<>();
 214             @SuppressWarnings("rawtypes")
 215             List<TaxonBase> taxa = getTaxonService().find(taxonIdSet);
 216             taxa.stream().forEach(t->taxonMap.put(t.getUuid().toString(), t));
 217             result.put(nameSpace, taxonMap);
 218
 219                         //reference map
 220                         nameSpace = MexicoEfloraRefArticlesImport.NAMESPACE;
 221                         idSet = referenceIdSet;
 222                         Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 223                         result.put(nameSpace, referenceMap);
 224
 225                 } catch (SQLException e) {
 226                         throw new RuntimeException(e);
 227                 }
 228                 return result;
 229         }
 230
 231         @Override
 232         protected String getTableName() {
 233                 return dbTableName;
 234         }
 235
 236         @Override
 237         public String getPluralString() {
 238                 return pluralString;
 239         }
 240
 241     @Override
 242     protected boolean doCheck(MexicoEfloraImportState state){
 243         return true;
 244     }
 245
 246         @Override
 247         protected boolean isIgnore(MexicoEfloraImportState state){
 248                 return ! state.getConfig().isDoTaxa();
 249         }
 250 }