app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraTaxonImport.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
  10 package eu.etaxonomy.cdm.io.mexico;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.commons.lang.StringUtils;
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelReferenceImport;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameImport;
  25 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  26 import eu.etaxonomy.cdm.model.common.CdmBase;
  27 import eu.etaxonomy.cdm.model.common.Language;
  28 import eu.etaxonomy.cdm.model.description.Feature;
  29 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  30 import eu.etaxonomy.cdm.model.description.TextData;
  31 import eu.etaxonomy.cdm.model.name.Rank;
  32 import eu.etaxonomy.cdm.model.name.TaxonName;
  33 import eu.etaxonomy.cdm.model.reference.Reference;
  34 import eu.etaxonomy.cdm.model.taxon.Synonym;
  35 import eu.etaxonomy.cdm.model.taxon.Taxon;
  36 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  37 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  38 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  39
  40
  41 /**
  42  * @author a.mueller
  43  * @since 20.03.2008
  44  */
  45 @Component
  46 public class MexicoEfloraTaxonImport  extends MexicoEfloraImportBase {
  47
  48     private static final long serialVersionUID = -1186364983750790695L;
  49
  50     private static final Logger logger = Logger.getLogger(MexicoEfloraTaxonImport.class);
  51
  52         public static final String NAMESPACE = "Taxon";
  53
  54         private static final String pluralString = "Taxa";
  55         private static final String dbTableName = "Efloa_Taxonomia4CDM2 ";
  56
  57
  58         /**
  59          * How should the publish flag in table PTaxon be interpreted
  60          * NO_MARKER: No marker is set
  61          * ONLY_FALSE:
  62          */
  63         public enum PublishMarkerChooser{
  64                 NO_MARKER,
  65                 ONLY_FALSE,
  66                 ONLY_TRUE,
  67                 ALL;
  68
  69                 boolean doMark(boolean value){
  70                         if (value == true){
  71                                 return this == ALL || this == ONLY_TRUE;
  72                         }else{
  73                                 return this == ALL || this == ONLY_FALSE;
  74                         }
  75                 }
  76         }
  77
  78         public MexicoEfloraTaxonImport(){
  79                 super(dbTableName, pluralString);
  80         }
  81
  82         @Override
  83         protected String getIdQuery(MexicoEfloraImportState state) {
  84                 String sql = " SELECT IdCAT "
  85                         + " FROM " + dbTableName
  86                         + " ORDER BY IdCAT ";
  87                 return sql;
  88         }
  89
  90         @Override
  91         protected String getRecordQuery(MexicoEfloraImportConfigurator config) {
  92                 String sqlSelect = " SELECT * ";
  93                 String sqlFrom = " FROM " + dbTableName;
  94                 String sqlWhere = " WHERE ( IdCAT IN (" + ID_LIST_TOKEN + ") )";
  95
  96                 String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere ;
  97                 return strRecordQuery;
  98         }
  99
 100         @Override
 101         protected boolean doCheck(MexicoEfloraImportState state){
 102                 //IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonImportValidator();
 103                 //return validator.validate(state);
 104             return true;
 105         }
 106
 107         @Override
 108         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, MexicoEfloraImportState state) {
 109
 110             boolean success = true ;
 111             MexicoEfloraImportConfigurator config = state.getConfig();
 112                 @SuppressWarnings("rawtypes")
 113         Set<TaxonBase> taxaToSave = new HashSet<>();
 114 //              @SuppressWarnings("unchecked")
 115 //        Map<String, TaxonName> taxonNameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
 116                 @SuppressWarnings("unchecked")
 117         Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
 118
 119                 ResultSet rs = partitioner.getResultSet();
 120                 try{
 121                         while (rs.next()){
 122
 123                         //      if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
 124
 125                                 //create TaxonName element
 126                                 String taxonId = rs.getString("IdCAT");
 127                                 String status = rs.getString("EstatusNombre");
 128                                 String rankStr = rs.getString("CategoriaTaxonomica");
 129                                 String nameStr = rs.getString("Nombre");
 130                                 String autorStr = rs.getString("AutorSinAnio");
 131                                 String fullNameStr = nameStr + " " + autorStr;
 132                             String annotationStr = rs.getString("AnotacionTaxon");
 133 //                          String type = rs.getString("NomPublicationType");
 134                             String year = rs.getString("Anio");
 135                                 int secFk = rs.getInt("IdBibliografiaSec");
 136                             int nameId = rs.getInt("idNombre");
 137
 138
 139                                 //IdCATRel => Accepted Taxon => TaxonRel
 140                                 //IdCAT_AscendenteHerarquico4CDM => Parent => TaxonRel
 141                                 //IdCAT_BasNomOrig => Basionyme der akzeptierten Taxa => TaxonRel
 142
 143                                 Rank rank = Rank.GENUS(); //FIXME
 144                                 NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 145                                 TaxonName taxonName = (TaxonName)parser.parseFullName(fullNameStr);
 146
 147                                 String refFkStr = String.valueOf(secFk);
 148                                 Reference sec = refMap.get(refFkStr);
 149
 150                                 TaxonBase<?> taxonBase;
 151                                 Synonym synonym;
 152                                 Taxon taxon;
 153                                 try {
 154                                         if ("aceptado".equals(status)){
 155                                                 taxon = Taxon.NewInstance(taxonName, sec);
 156                                                 taxonBase = taxon;
 157                                         }else if ("sinónimo".equals(status)){
 158                                                 synonym = Synonym.NewInstance(taxonName, sec);
 159                                                 taxonBase = synonym;
 160                                         }else {
 161                                             taxonBase = null;
 162                                             logger.error("Status not yet implemented: " + status);
 163                                             return false;
 164                                         }
 165
 166                                         DefinedTerm taxonIdType = DefinedTerm.IDENTIFIER_NAME_IPNI();
 167                                         taxonBase.addIdentifier(taxonId, taxonIdType);
 168
 169                                         //namePhrase
 170                                         String namePhrase = rs.getString("NamePhrase");
 171                                         if (StringUtils.isNotBlank(namePhrase)){
 172                                                 taxonBase.setAppendedPhrase(namePhrase);
 173                                         }
 174
 175                                         //Notes
 176 //                                      boolean excludeNotes = state.getConfig().isTaxonNoteAsFeature() && taxonBase.isInstanceOf(Taxon.class);
 177 //                                      String notes = rs.getString("Notes");
 178
 179 //                                      doIdCreatedUpdatedNotes(state, taxonBase, rs, taxonId, NAMESPACE, false);
 180 //                                      if (excludeNotes && notes != null){
 181 //                                          makeTaxonomicNote(state, CdmBase.deproxy(taxonBase, Taxon.class), rs.getString("Notes"));
 182 //                                      }
 183
 184                                         partitioner.startDoSave();
 185                                         taxaToSave.add(taxonBase);
 186                                 } catch (Exception e) {
 187                                         logger.warn("An exception (" +e.getMessage()+") occurred when creating taxon with id " + taxonId + ". Taxon could not be saved.");
 188                                         success = false;
 189                                 }
 190                         }
 191                 } catch (Exception e) {
 192                         logger.error("SQLException:" +  e);
 193                         return false;
 194                 }
 195
 196                 getTaxonService().save(taxaToSave);
 197                 return success;
 198         }
 199
 200     @Override
 201     protected String getIdInSource(MexicoEfloraImportState state, ResultSet rs) throws SQLException {
 202         String id = rs.getString("idInSource");
 203         return id;
 204     }
 205
 206     private void makeTaxonomicNote(MexicoEfloraImportState state, Taxon taxon, String notes) {
 207         if (isNotBlank(notes)){
 208             TaxonDescription desc = getTaxonDescription(taxon, false, true);
 209             desc.setDefault(true);  //hard coded for Salvador, not used elsewhere as far as I can see
 210             TextData textData = TextData.NewInstance(Feature.NOTES() , notes, Language.SPANISH_CASTILIAN(), null);
 211             desc.addElement(textData);
 212         }
 213     }
 214
 215     @Override
 216         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, MexicoEfloraImportState state) {
 217
 218         String nameSpace;
 219                 Set<String> idSet;
 220                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 221
 222                 try{
 223                         Set<String> nameIdSet = new HashSet<>();
 224                         Set<String> referenceIdSet = new HashSet<>();
 225                         while (rs.next()){
 226                                 handleForeignKey(rs, nameIdSet, "PTNameFk");
 227                                 handleForeignKey(rs, referenceIdSet, "PTRefFk");
 228                         }
 229
 230                         //name map
 231                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 232                         idSet = nameIdSet;
 233                         Map<String, TaxonName> nameMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
 234                         result.put(nameSpace, nameMap);
 235
 236                         //reference map
 237                         nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
 238                         idSet = referenceIdSet;
 239                         Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 240                         result.put(nameSpace, referenceMap);
 241
 242                 } catch (SQLException e) {
 243                         throw new RuntimeException(e);
 244                 }
 245                 return result;
 246         }
 247
 248         @Override
 249         protected String getTableName() {
 250                 return dbTableName;
 251         }
 252
 253         @Override
 254         public String getPluralString() {
 255                 return pluralString;
 256         }
 257
 258         @Override
 259         protected boolean isIgnore(MexicoEfloraImportState state){
 260                 return ! state.getConfig().isDoTaxa();
 261         }
 262 }