cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonRelationImport.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.pesi.erms;
  12
  13 import java.sql.ResultSet;
  14 import java.sql.SQLException;
  15 import java.util.HashMap;
  16 import java.util.HashSet;
  17 import java.util.Map;
  18 import java.util.Set;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  24 import eu.etaxonomy.cdm.io.common.mapping.DbImportNameTypeDesignationMapper;
  25 import eu.etaxonomy.cdm.io.common.mapping.DbImportSynonymMapper;
  26 import eu.etaxonomy.cdm.io.common.mapping.DbImportTaxIncludedInMapper;
  27 import eu.etaxonomy.cdm.io.common.mapping.ICheckIgnoreMapper;
  28 import eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper;
  29 import eu.etaxonomy.cdm.model.common.CdmBase;
  30 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  33
  34 /**
  35  * @author a.mueller
  36  * @created 09.03.2010
  37  */
  38 @Component
  39 public class ErmsTaxonRelationImport extends ErmsImportBase<TaxonBase<?>> implements ICheckIgnoreMapper{
  40         @SuppressWarnings("unused")
  41         private static final Logger logger = Logger.getLogger(ErmsTaxonRelationImport.class);
  42
  43         private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping;
  44
  45         private static final String pluralString = "taxon relations";
  46         private static final String dbTableName = "tu";
  47
  48         private static final Class<?> cdmTargetClass = TaxonBase.class;
  49
  50         private ErmsImportState state;  //ERMS import will never run in more then one instance
  51
  52         public ErmsTaxonRelationImport(){
  53                 super(pluralString, dbTableName, cdmTargetClass);
  54         }
  55
  56
  57         @Override
  58         protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
  59                 if (mapping == null){
  60                         mapping = new DbImportMapping<ErmsImportState, ErmsImportConfigurator>();
  61
  62                         mapping.addMapper(DbImportTaxIncludedInMapper.NewInstance("id", TAXON_NAMESPACE, "parentId", TAXON_NAMESPACE, "accParentId", TAXON_NAMESPACE, null));//there is only one tree
  63
  64                         TaxonRelationshipType taxonRelationshipType = getTaxonRelationshipType(state, ErmsTransformer.uuidTaxRelTypeIsTaxonSynonymOf, "is taxon synonym of", "is synonym of relation used by synonym that are of class Taxon as they can not be handled differently", null, null);
  65                         mapping.addMapper(DbImportSynonymMapper.NewInstance("id", "tu_acctaxon", TAXON_NAMESPACE, null, taxonRelationshipType));
  66                         mapping.addMapper(DbImportNameTypeDesignationMapper.NewInstance("id", "tu_typetaxon", ErmsTaxonImport.NAME_NAMESPACE, "tu_typedesignationstatus"));
  67 //                      mapping.addMapper(DbNotYetImplementedMapper.NewInstance("tu_acctaxon"));
  68                 }
  69                 return mapping;
  70         }
  71
  72
  73         /* (non-Javadoc)
  74          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.erms.ErmsImportConfigurator)
  75          */
  76         protected String getRecordQuery(ErmsImportConfigurator config) {
  77                 //TODO get automatic by second path mappers
  78                 String selectAttributes = " myTaxon.id, myTaxon.tu_parent, myTaxon.tu_typetaxon, myTaxon.tu_typedesignation, " +
  79                                                                 " myTaxon.tu_acctaxon, myTaxon.tu_status, parent.tu_status AS parentStatus, parent.id AS parentId, " +
  80                                                                 " accParent.tu_status AS accParentStatus, accParent.id AS accParentId ";
  81                 String strRecordQuery =
  82                         " SELECT  " + selectAttributes +
  83                         " FROM tu AS myTaxon LEFT OUTER JOIN " +
  84                                 " tu AS accTaxon ON myTaxon.tu_acctaxon = accTaxon.id LEFT OUTER JOIN " +
  85                                 " tu AS accParent RIGHT OUTER JOIN "  +
  86                                 " tu AS parent ON accParent.id = parent.tu_acctaxon ON myTaxon.tu_parent = parent.id " +
  87                         " WHERE ( myTaxon.id IN (" + ID_LIST_TOKEN + ") )";
  88                 return strRecordQuery;
  89         }
  90
  91
  92         @Override
  93         protected void doInvoke(ErmsImportState state) {
  94                 this.state = state;
  95                 super.doInvoke(state);
  96         }
  97
  98         @Override
  99         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, ErmsImportState state) {
 100                 String nameSpace;
 101                 Class<?> cdmClass;
 102                 Set<String> idSet;
 103                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 104
 105                 try{
 106                         Set<String> taxonIdSet = new HashSet<String>();
 107                         Set<String> nameIdSet = new HashSet<String>();
 108                         while (rs.next()){
 109                                 handleForeignKey(rs, taxonIdSet, "parentId");
 110                                 handleForeignKey(rs, taxonIdSet, "accParentId");
 111                                 handleForeignKey(rs, taxonIdSet, "tu_acctaxon");
 112                                 handleForeignKey(rs, taxonIdSet, "id");
 113                                 handleForeignKey(rs, nameIdSet, "tu_typetaxon");
 114                                 handleForeignKey(rs, nameIdSet, "id");
 115                         }
 116
 117                         //name map
 118                         nameSpace = ErmsTaxonImport.NAME_NAMESPACE;
 119                         cdmClass = TaxonNameBase.class;
 120                         idSet = nameIdSet;
 121                         Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 122                         result.put(nameSpace, nameMap);
 123
 124
 125                         //taxon map
 126                         nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
 127                         cdmClass = TaxonBase.class;
 128                         idSet = taxonIdSet;
 129                         Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 130                         result.put(nameSpace, taxonMap);
 131
 132                 } catch (SQLException e) {
 133                         throw new RuntimeException(e);
 134                 }
 135                 return result;
 136         }
 137
 138
 139         /* (non-Javadoc)
 140          * @see eu.etaxonomy.cdm.io.erms.ICheckIgnoreMapper#checkIgnoreMapper(eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper, java.sql.ResultSet)
 141          */
 142         public boolean checkIgnoreMapper(IDbImportMapper mapper, ResultSet rs) throws SQLException{
 143                 boolean result = false;
 144                 if (mapper instanceof DbImportTaxIncludedInMapper){
 145                         //old
 146 //                      int tu_status = rs.getInt("tu_status");
 147 //                      if (tu_status != 1){
 148 //                              result = true;
 149 //                      }
 150
 151                         int id = rs.getInt("id");
 152                         if (state.getAcceptedTaxaKeys().contains(id)){
 153                                 return false;
 154                         }else{
 155                                 return true;
 156                         }
 157                 }else if (mapper instanceof DbImportSynonymMapper){
 158                         //old
 159 //                      int tu_status = rs.getInt("tu_status");
 160 //                      if (tu_status == 1){
 161 //                              result = true;
 162 //                      }else{
 163 //                              return false;
 164 //                      }t.tu_acctaxon <> t.id
 165
 166                         int id = rs.getInt("id");
 167                         Object accTaxonId = rs.getObject("tu_acctaxon");
 168                         if (accTaxonId == null){
 169                                 return true;
 170                         }else{
 171                                 int accId = Integer.valueOf(String.valueOf(accTaxonId));
 172                                 return accId == id;
 173                         }
 174                 }else if (mapper instanceof DbImportNameTypeDesignationMapper){
 175                         Object tu_typeTaxon = rs.getObject("tu_typetaxon");
 176                         if (tu_typeTaxon == null){
 177                                 return true;
 178                         }
 179                 }
 180                 return result;
 181         }
 182
 183
 184         @Override
 185         protected boolean doCheck(ErmsImportState state){
 186 //              IOValidator<ErmsImportState> validator = new ErmsTaxonImportValidator();
 187 //              return validator.validate(state);
 188                 return true;
 189         }
 190
 191         @Override
 192         protected boolean isIgnore(ErmsImportState state){
 193                 return ! state.getConfig().isDoRelTaxa();
 194         }
 195
 196
 197
 198 }