app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.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.caryo;
  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.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21
  22 import eu.etaxonomy.cdm.io.common.DbImportBase;
  23 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  24 import eu.etaxonomy.cdm.io.common.Source;
  25 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  26 import eu.etaxonomy.cdm.model.common.CdmBase;
  27 import eu.etaxonomy.cdm.model.common.Language;
  28 import eu.etaxonomy.cdm.model.name.BotanicalName;
  29 import eu.etaxonomy.cdm.model.name.Rank;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.taxon.Classification;
  32 import eu.etaxonomy.cdm.model.taxon.Taxon;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  34
  35
  36 /**
  37  * @author a.mueller
  38  * @created 20.02.2010
  39  * @version 1.0
  40  */
  41 @Component
  42 public class CaryoTaxonImport  extends DbImportBase<CaryoImportState, CaryoImportConfigurator> {
  43         private static final Logger logger = Logger.getLogger(CaryoTaxonImport.class);
  44
  45         private int modCount = 10000;
  46         private static final String pluralString = "taxa";
  47         private static final String dbTableName = "CARYOPHYLLALES";
  48         private static final String FAMILY = "Family";
  49         private static final String PERSON = "Person";
  50         private static final String TEAM = "Team";
  51         private static final String JOURNAL = "Journal";
  52         private static final String BOOK = "Book";
  53
  54
  55         private Map<String, Taxon> familyMap = new HashMap<String, Taxon>();
  56         private Map<String, TeamOrPersonBase> personMap = new HashMap<String, TeamOrPersonBase>();
  57         private Map<String, TeamOrPersonBase> teamMap = new HashMap<String, TeamOrPersonBase>();
  58         private Map<String, Reference> journalMap = new HashMap<String, Reference>();
  59         private Map<String, Reference> bookMap = new HashMap<String, Reference>();
  60
  61
  62         private Classification classification;
  63
  64
  65         public CaryoTaxonImport(){
  66                 super(pluralString, dbTableName);
  67         }
  68
  69
  70
  71
  72         /* (non-Javadoc)
  73          * @see eu.etaxonomy.cdm.io.common.DbImportBase#getIdQuery(eu.etaxonomy.cdm.io.common.DbImportStateBase)
  74          */
  75         @Override
  76         protected String getIdQuery(CaryoImportState state) {
  77                 String strRecordQuery =
  78                         " SELECT ID " +
  79                         " FROM " + dbTableName;
  80                 return strRecordQuery;
  81         }
  82
  83
  84         /* (non-Javadoc)
  85          * @see eu.etaxonomy.cdm.io.common.DbImportBase#getRecordQuery(eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase)
  86          */
  87         @Override
  88         protected String getRecordQuery(CaryoImportConfigurator config) {
  89                 String strRecordQuery =
  90                         " SELECT cs.* " +
  91                         " FROM " + getTableName() + " t " +
  92                         " WHERE ( t.ID IN (" + ID_LIST_TOKEN + ") )";
  93                 return strRecordQuery;
  94         }
  95
  96
  97
  98         /* (non-Javadoc)
  99          * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)
 100          */
 101         @Override
 102         public boolean doPartition(ResultSetPartitioner partitioner, CaryoImportState state) {
 103                 boolean success = true;
 104
 105                 Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>();
 106
 107 //              Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);
 108
 109
 110                 classification = getClassification(state);
 111
 112                 try {
 113                         doFamilies(state);
 114                         doAuthors(state);
 115                         doJournals(state);
 116                         doBooks(state);
 117
 118                         ResultSet rs = partitioner.getResultSet();
 119
 120                         int i = 0;
 121
 122                         //for each reference
 123             while (rs.next()){
 124
 125                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 126
 127                         Integer taxonId = rs.getInt("IDcurrentspec");
 128
 129
 130                         //String dtSpcJahr -> ignore !
 131                         //empty: fiSpcLiteratur
 132
 133                         //TODO
 134                         //fiSpcspcgrptax
 135
 136
 137
 138                                 try {
 139
 140
 141 //                                      classification.addParentChild(nextHigherTaxon, species, sourceRef, null);
 142 //
 143 //
 144 //                                      this.doIdCreatedUpdatedNotes(state, species, rs, taxonId, TAXON_NAMESPACE);
 145 //
 146 //                                      objectsToSave.add(species);
 147
 148
 149                                 } catch (Exception e) {
 150                                         logger.warn("Exception in current_species: IDcurrentspec " + taxonId + ". " + e.getMessage());
 151 //                                      e.printStackTrace();
 152                                 }
 153
 154             }
 155
 156 //            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
 157
 158                         logger.warn(pluralString + " to save: " + objectsToSave.size());
 159                         getTaxonService().save(objectsToSave);
 160
 161                         return success;
 162                 } catch (SQLException e) {
 163                         logger.error("SQLException:" +  e);
 164                         return false;
 165                 }
 166         }
 167
 168
 169
 170
 171
 172
 173
 174         private void doAuthors(CaryoImportState state) {
 175                 // TODO Auto-generated method stub
 176
 177         }
 178
 179
 180
 181
 182         private void doBooks(CaryoImportState state) {
 183                 // TODO Auto-generated method stub
 184
 185         }
 186
 187
 188
 189
 190         private void doJournals(CaryoImportState state) {
 191                 // TODO Auto-generated method stub
 192
 193         }
 194
 195
 196
 197
 198         private void doFamilies(CaryoImportState state) throws SQLException {
 199                 Source source = state.getConfig().getSource();
 200                 String sqlFamily = "SELECT DISTINCT family FROM table WHERE family IS NOT NULL";
 201                 ResultSet rs = source.getResultSet(sqlFamily);
 202                 while (rs.next()){
 203                         String family = rs.getString("family");
 204                         BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());
 205                         name.setGenusOrUninomial(family);
 206                         Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());
 207                         classification.addChildTaxon(taxon, null, null, null);
 208 //                      taxon.addSource(id, idNamespace, citation, null);
 209
 210
 211                         familyMap.put(family, taxon);
 212                 }
 213
 214         }
 215
 216         private Classification getClassification(CaryoImportState state) {
 217                 if (this.classification == null){
 218                         String name = state.getConfig().getClassificationName();
 219                         Reference<?> reference = state.getTransactionalSourceReference();
 220                         this.classification = Classification.NewInstance(name, reference, Language.DEFAULT());
 221                         if (state.getConfig().getClassificationUuid() != null){
 222                                 classification.setUuid(state.getConfig().getClassificationUuid());
 223                         }
 224                         getClassificationService().save(classification);
 225                 }
 226                 return this.classification;
 227
 228         }
 229
 230
 231
 232
 233
 234         /* (non-Javadoc)
 235          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 236          */
 237         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 238 //              String nameSpace;
 239 //              Class cdmClass;
 240 //              Set<String> idSet;
 241                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 242 //              try{
 243 //                      Set<String> taxonIdSet = new HashSet<String>();
 244 //
 245 //                      while (rs.next()){
 246 ////                            handleForeignKey(rs, taxonIdSet, "taxonId");
 247 //                      }
 248 //
 249 //                      //taxon map
 250 //                      nameSpace = TAXON_NAMESPACE;
 251 //                      cdmClass = Taxon.class;
 252 //                      idSet = taxonIdSet;
 253 //                      Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 254 //                      result.put(nameSpace, objectMap);
 255 //
 256 //
 257 //              } catch (SQLException e) {
 258 //                      throw new RuntimeException(e);
 259 //              }
 260                 return result;
 261         }
 262
 263         /* (non-Javadoc)
 264          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 265          */
 266         @Override
 267         protected boolean doCheck(CaryoImportState state){
 268                 return true;
 269         }
 270
 271
 272         /* (non-Javadoc)
 273          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 274          */
 275         protected boolean isIgnore(CaryoImportState state){
 276                 return ! state.getConfig().isDoTaxa();
 277         }
 278
 279
 280
 281
 282
 283
 284
 285 }