app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/RoteListeDbTaxonImport.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.redlist;
  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 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.common.IOValidator;
  24 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  25 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  26 import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;
  27 import eu.etaxonomy.cdm.io.redlist.validation.RoteListeDbTaxonImportValidator;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.name.BotanicalName;
  30 import eu.etaxonomy.cdm.model.name.Rank;
  31 import eu.etaxonomy.cdm.model.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  34
  35
  36 /**
  37  * TODO do we still need this class?
  38  * @author a.mueller
  39  * @created 27.08.2012
  40  */
  41 @Component
  42 public class RoteListeDbTaxonImport  extends RoteListeDbImportBase<TaxonBase> implements IMappingImport<TaxonBase, RoteListeDbImportState>{
  43         @SuppressWarnings("unused")
  44         private static final Logger logger = Logger.getLogger(RoteListeDbTaxonImport.class);
  45
  46         private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
  47
  48         private Map<UUID, Taxon> higherTaxonMap;
  49
  50         private Integer TREE_ID = null;
  51
  52         private DbImportMapping mapping;
  53
  54         private int modCount = 10000;
  55         private static final String pluralString = "taxa";
  56         private static final String dbTableName = "checklist";
  57         private static final Class cdmTargetClass = TaxonBase.class;
  58         private static final String strOrderBy = " ORDER BY family, genus, species ";
  59
  60         public RoteListeDbTaxonImport(){
  61                 super(pluralString, dbTableName, cdmTargetClass);
  62         }
  63
  64
  65         @Override
  66         protected String getIdQuery() {
  67                 String strQuery = " SELECT pk FROM " + dbTableName +
  68                                                 strOrderBy;
  69                 return strQuery;
  70         }
  71
  72         @Override
  73         protected DbImportMapping getMapping() {
  74                 if (mapping == null){
  75                         mapping = new DbImportMapping();
  76
  77 //                      mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "pk", TAXON_NAMESPACE)); //id + tu_status
  78 //
  79 //                      UUID uuidKew = RoteListeDbTransformer.uuidAcceptedKew;
  80 //                      mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted kew", uuidKew, "Accepted Kew", "Accepted Kew", "Kew", null));
  81
  82                 }
  83
  84                 return mapping;
  85         }
  86
  87         @Override
  88         protected String getRecordQuery(RoteListeDbImportConfigurator config) {
  89                 String strSelect = " SELECT * ";
  90                 String strFrom = " FROM checklist";
  91                 String strWhere = " WHERE ( pk IN (" + ID_LIST_TOKEN + ") )";
  92                 String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy;
  93                 return strRecordQuery;
  94         }
  95
  96
  97         @Override
  98         public boolean doPartition(ResultSetPartitioner partitioner, RoteListeDbImportState state) {
  99                 boolean success = super.doPartition(partitioner, state);
 100 //              higherTaxonMap = new HashMap<UUID, Taxon>();
 101 //              state.setGenevaReference(null);
 102                 return success;
 103         }
 104
 105
 106         @Override
 107         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, RoteListeDbImportState state) {
 108                 String nameSpace;
 109                 Class<?> cdmClass;
 110                 Set<String> idSet;
 111                 Set<String> referenceIdSet = new HashSet<String>();
 112
 113                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 114
 115                 try{
 116                         while (rs.next()){
 117                                 handleForeignKey(rs, referenceIdSet, "source");
 118                         }
 119
 120 //                      //reference map
 121 //                      nameSpace = REFERENCE_NAMESPACE;
 122 //                      cdmClass = Reference.class;
 123 //                      idSet = referenceIdSet;
 124 //                      Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, referenceIdSet, nameSpace);
 125 //                      result.put(REFERENCE_NAMESPACE, referenceMap);
 126
 127                 } catch (SQLException e) {
 128                         throw new RuntimeException(e);
 129                 }
 130                 return result;
 131         }
 132
 133
 134         @Override
 135         public TaxonBase createObject(ResultSet rs, RoteListeDbImportState state) throws SQLException {
 136                 BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES());
 137
 138 //              Reference sec = state.getConfig().getSourceReference();
 139 //              getReferenceService().saveOrUpdate(sec);
 140 //
 141 //              String familyString = rs.getString("family");
 142 //              String genusString = rs.getString("genus");
 143 //              String speciesString = rs.getString("species");
 144 //              String authorityString = rs.getString("authority");
 145 //
 146 //              if (logger.isDebugEnabled()){
 147 //                      System.out.println(familyString + " " + genusString + " " + speciesString);
 148 //              }
 149 //
 150 //              Taxon speciesTaxon = Taxon.NewInstance(speciesName, sec);;
 151 //              speciesName.setGenusOrUninomial(genusString);
 152 //              speciesName.setSpecificEpithet(speciesString);
 153 //              parser.handleAuthors(speciesName, CdmUtils.concat(" ", new String[] {"", genusString, speciesString, authorityString}), authorityString);
 154 //
 155 //              //family
 156 //              Taxon familyTaxon = null;
 157 //              if (StringUtils.isNotBlank(familyString)){
 158 //                      familyTaxon = getHigherTaxon(state, familyString, null);
 159 //                      if (familyTaxon == null){
 160 //                              BotanicalName familyName = BotanicalName.NewInstance(Rank.FAMILY());
 161 //                              familyName.setGenusOrUninomial(familyString);
 162 //                              familyTaxon = Taxon.NewInstance(familyName, sec);
 163 //                              saveHigherTaxon(state, familyTaxon, familyString, null);
 164 //                      }
 165 //                      getTaxonService().saveOrUpdate(familyTaxon);
 166 //              }
 167 //
 168 //
 169 //              //genus
 170 //              Taxon genusTaxon = getHigherTaxon(state, familyString, genusString);
 171 //              if (genusTaxon == null){
 172 //                      BotanicalName genusName = BotanicalName.NewInstance(Rank.GENUS());
 173 //                      genusName.setGenusOrUninomial(genusString);
 174 //                      genusTaxon = Taxon.NewInstance(genusName, sec);
 175 //                      saveHigherTaxon(state, genusTaxon, familyString, genusString);
 176 //                      if (familyTaxon != null){
 177 //                              makeTaxonomicallyIncluded(state, TREE_ID, genusTaxon, familyTaxon, null, null);
 178 //                      }
 179 //              }
 180 //              makeTaxonomicallyIncluded(state, TREE_ID, speciesTaxon, genusTaxon, null, null);
 181 //              getTaxonService().saveOrUpdate(genusTaxon);
 182 //
 183 //              String sourceString = rs.getString("source");
 184 //              String sourceId = rs.getString("source_id");
 185 //
 186 //              Reference sourceRef = state.getRelatedObject(REFERENCE_NAMESPACE, sourceString, Reference.class);
 187 //              speciesTaxon.addSource(sourceId, REFERENCE_NAMESPACE, sourceRef, null);
 188 //
 189 //
 190 //              //distribution
 191 //              handleDistribution(rs, speciesTaxon);
 192 //
 193 //              return speciesTaxon;
 194
 195                 return null;
 196         }
 197
 198
 199         @Override
 200         protected boolean doCheck(RoteListeDbImportState state){
 201                 IOValidator<RoteListeDbImportState> validator = new RoteListeDbTaxonImportValidator();
 202                 return validator.validate(state);
 203         }
 204
 205
 206         @Override
 207         protected boolean isIgnore(RoteListeDbImportState state){
 208                 return ! state.getConfig().isDoTaxa();
 209         }
 210
 211
 212
 213 }