cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistSynonymImport.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.eflora.centralAfrica.checklist;
  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.common.CdmUtils;
  23 import eu.etaxonomy.cdm.io.common.IOValidator;
  24 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  25 import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectCreationMapper;
  26 import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;
  27 import eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.validation.CentralAfricaChecklistTaxonImportValidator;
  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.reference.Reference;
  32 import eu.etaxonomy.cdm.model.taxon.Synonym;
  33 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  34 import eu.etaxonomy.cdm.model.taxon.Taxon;
  35 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  36 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  37
  38
  39 /**
  40  * @author a.mueller
  41  * @created 20.02.2010
  42  * @version 1.0
  43  */
  44 @Component
  45 public class CentralAfricaChecklistSynonymImport  extends CentralAfricaChecklistImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaChecklistImportState>{
  46         private static final Logger logger = Logger.getLogger(CentralAfricaChecklistSynonymImport.class);
  47
  48         private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
  49
  50
  51         private DbImportMapping mapping;
  52
  53         //second path is not used anymore, there is now an ErmsTaxonRelationImport class instead
  54         private boolean isSecondPath = false;
  55
  56         private int modCount = 10000;
  57         private static final String pluralString = "synonyms";
  58         private static final String dbTableName = "synonyms";
  59         private static final Class cdmTargetClass = TaxonBase.class;
  60         private static final String strOrderBy = "";
  61
  62         public CentralAfricaChecklistSynonymImport(){
  63                 super(pluralString, dbTableName, cdmTargetClass);
  64         }
  65
  66
  67
  68         /* (non-Javadoc)
  69          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()
  70          */
  71         @Override
  72         protected String getIdQuery() {
  73                 String strQuery = " SELECT syn_id FROM " + dbTableName + strOrderBy;
  74                 return strQuery;
  75         }
  76
  77
  78         /* (non-Javadoc)
  79          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
  80          */
  81         protected DbImportMapping getMapping() {
  82                 if (mapping == null){
  83                         mapping = new DbImportMapping();
  84
  85                         mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "syn_id", SYNONYM_NAMESPACE));
  86                         //TODO Synonym mapper gibts es auch
  87
  88                 }
  89                 return mapping;
  90         }
  91
  92         /* (non-Javadoc)
  93          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  94          */
  95         @Override
  96         protected String getRecordQuery(CentralAfricaChecklistImportConfigurator config) {
  97                 String strSelect = " SELECT * ";
  98                 String strFrom = " FROM " + dbTableName;
  99                 String strWhere = " WHERE ( syn_id IN (" + ID_LIST_TOKEN + ") )";
 100                 String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy;
 101                 return strRecordQuery;
 102         }
 103
 104
 105         /* (non-Javadoc)
 106          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 107          */
 108         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 109                 String nameSpace;
 110                 Class cdmClass;
 111                 Set<String> idSet;
 112                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 113
 114                 try{
 115                                 Set<String> taxonIdSet = new HashSet<String>();
 116                                 while (rs.next()){
 117                                         handleForeignKey(rs, taxonIdSet, "acc_id");
 118                                 }
 119
 120                         //taxon map
 121                         nameSpace = TAXON_NAMESPACE;
 122                         cdmClass = Taxon.class;
 123                         idSet = taxonIdSet;
 124                         Map<String, Taxon> taxonMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 125                         result.put(nameSpace, taxonMap);
 126
 127                 } catch (SQLException e) {
 128                         throw new RuntimeException(e);
 129                 }
 130                 return result;
 131         }
 132
 133
 134         /* (non-Javadoc)
 135          * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet)
 136          */
 137         public TaxonBase createObject(ResultSet rs, CentralAfricaChecklistImportState state) throws SQLException {
 138                 BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES());
 139
 140
 141                 Integer accId = rs.getInt("acc_id");
 142                 Taxon taxon = CdmBase.deproxy(state.getRelatedObject(TAXON_NAMESPACE, String.valueOf(accId)), Taxon.class);
 143
 144                 Reference sec = taxon.getSec();
 145
 146                 String genusString = rs.getString("synonym genus");
 147                 String speciesString = rs.getString("synonym species");
 148                 String authorityString = rs.getString("synonym authority");
 149
 150                 Synonym synonym = Synonym.NewInstance(speciesName, sec);
 151
 152                 speciesName.setGenusOrUninomial(genusString);
 153                 speciesName.setSpecificEpithet(speciesString);
 154                 parser.handleAuthors(speciesName, CdmUtils.concat(" ", new String[] {"", genusString, speciesString, authorityString}), authorityString);
 155
 156                 if (taxon != null){
 157                         taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
 158                 }else{
 159                         logger.warn("Taxon (" + accId + ") not available for Synonym " + synonym.getTitleCache());
 160                 }
 161                 return synonym;
 162         }
 163
 164
 165         /* (non-Javadoc)
 166          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 167          */
 168         @Override
 169         protected boolean doCheck(CentralAfricaChecklistImportState state){
 170                 IOValidator<CentralAfricaChecklistImportState> validator = new CentralAfricaChecklistTaxonImportValidator();
 171                 return validator.validate(state);
 172         }
 173
 174
 175         /* (non-Javadoc)
 176          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 177          */
 178         protected boolean isIgnore(CentralAfricaChecklistImportState state){
 179                 return ! state.getConfig().isDoTaxa();
 180         }
 181
 182
 183
 184 }