cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaHeterotypicSynonymImport.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.io.faunaEuropaea;
  12
  13 import java.util.Collection;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Set;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.stereotype.Component;
  20 import org.springframework.transaction.TransactionStatus;
  21
  22 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  23 import eu.etaxonomy.cdm.io.common.ICdmImport;
  24 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  25 import eu.etaxonomy.cdm.model.name.NameRelationship;
  26 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  27 import eu.etaxonomy.cdm.model.taxon.Synonym;
  28 import eu.etaxonomy.cdm.model.taxon.Taxon;
  29 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  30
  31 /**
  32  * This class creates heterotypic synonymy relationships to the accepted taxon for
  33  * basionym synonyms.
  34  *
  35  * @author a.babadshanjan
  36  * @created 22.09.2009
  37  * @version 1.0
  38  */
  39 @Component
  40 public class FaunaEuropaeaHeterotypicSynonymImport extends CdmImportBase<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState>
  41 implements ICdmImport<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState> {
  42         private static final Logger logger = Logger
  43                         .getLogger(FaunaEuropaeaHeterotypicSynonymImport.class);
  44
  45         /* (non-Javadoc)
  46          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
  47          */
  48         @Override
  49         protected boolean doCheck(FaunaEuropaeaImportState state) {
  50                 logger.warn("Checking for heterotypic synonyms for basionyms not yet implemented");
  51                 return false;
  52         }
  53
  54         /* (non-Javadoc)
  55          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)
  56          */
  57         @Override
  58         protected boolean doInvoke(FaunaEuropaeaImportState state) {
  59
  60                 TransactionStatus txStatus = null;
  61                 List<Synonym> synonymList = null;
  62                 Set<Taxon> taxonSet = null;
  63                 int i = 0;
  64                 int start = 0;
  65
  66                 int limit = state.getConfig().getLimitSave();
  67                 int nbrOfSynonyms = getTaxonService().count(Synonym.class);
  68                 if (logger.isInfoEnabled()) {
  69                         logger.info("Number of synonyms = " + nbrOfSynonyms);
  70                 }
  71
  72                 while (i < nbrOfSynonyms) {
  73
  74                         try {
  75                                 if ((i++ % limit) == 0) {
  76
  77                                         start = (i == 1) ? 0 : i;
  78                                         if (logger.isInfoEnabled()) {
  79                                                 logger.info("Retrieving synonyms starting from: " + start);
  80                                         }
  81                                         txStatus = startTransaction();
  82                                         synonymList = getTaxonService().getAllSynonyms(limit, start);
  83                                         taxonSet = new HashSet<Taxon>(limit);
  84                                 }
  85
  86                                 if (((i % limit) == 0 && i != 1 ) || i == nbrOfSynonyms) {
  87
  88                                         HomotypicalGroup homotypicalGroup = null;
  89                                         Set<TaxonNameBase> basionyms = null;
  90                                         Set<NameRelationship> nameRelations = null;
  91                                         TaxonNameBase basionym = null;
  92                                         Set<TaxonBase> taxonBases = null;
  93                                         TaxonBase taxonBase = null;
  94                                         Taxon acceptedTaxon = null;
  95                                         TaxonNameBase synonymName = null;
  96                                         NameRelationship nameRelation = null;
  97                                         TaxonNameBase acceptedName = null;
  98
  99                                         for (Synonym synonym : synonymList) {
 100                                                 synonymName = synonym.getName();
 101                                                 if (synonymName.isGroupsBasionym()) {
 102                                                         nameRelations = synonymName.getNameRelations();
 103                                                         if (nameRelations != null && nameRelations.iterator().hasNext()) {
 104                                                                 nameRelation = nameRelations.iterator().next();
 105                                                                 acceptedName = nameRelation.getToName();
 106                                                                 logger.info("SynonymName: " + synonymName + " titleCache of synonym: "+synonym.getTitleCache() + " name of acceptedTaxon: " + acceptedName.getTitleCache());
 107                                                                 if (logger.isTraceEnabled()) {
 108                                                                         logger.trace("toName: " + acceptedName);
 109                                                                         logger.trace("fromName: " + nameRelation.getFromName());
 110                                                                 }
 111                                                                 taxonBases = acceptedName.getTaxa();
 112                                                                 if (taxonBases != null && taxonBases.iterator().hasNext()) {
 113                                                                         taxonBase = taxonBases.iterator().next();
 114                                                                         acceptedTaxon = taxonBase.deproxy(taxonBase, Taxon.class);
 115                                                                         Set <Synonym> synonyms = acceptedTaxon.getSynonyms();
 116                                                                         if (!synonyms.contains(synonym)){
 117                                                                         //TODO: Achtung!!!!! dies wird auch bei homotypischen Synonymen aufgerufen! Dadurch wird ein weiteres Synonym erzeugt
 118                                                                                 acceptedTaxon.addHeterotypicSynonymName(synonymName);
 119                                                                                 taxonSet.add(acceptedTaxon);
 120                                                                         }
 121                                                                 }
 122                                                         }
 123                                                 }
 124                                         }
 125
 126                                         getTaxonService().save((Collection)taxonSet);
 127                                         taxonSet = null;
 128                                         synonymList = null;
 129                                         commitTransaction(txStatus);
 130                                         if(logger.isInfoEnabled()) {
 131                                                 logger.info("i = " + i + " - Transaction committed");
 132                                         }
 133                                 }
 134
 135                         } catch (Exception e) {
 136                                 logger.warn("An exception occurred when creating heterotypic synonym relationship # " + i );
 137                                 e.printStackTrace();
 138                         }
 139                 }
 140                 return true;
 141         }
 142
 143         /* (non-Javadoc)
 144          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
 145          */
 146         @Override
 147         protected boolean isIgnore(FaunaEuropaeaImportState state) {
 148                 return !(state.getConfig().isDoHeterotypicSynonymsForBasionyms());
 149         }
 150 }