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
  33 /**
  34  * @author a.mueller
  35  * @created 09.03.2010
  36  * @version 1.0
  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         /* (non-Javadoc)
  57          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
  58          */
  59         protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
  60                 if (mapping == null){
  61                         mapping = new DbImportMapping<ErmsImportState, ErmsImportConfigurator>();
  62
  63                         mapping.addMapper(DbImportTaxIncludedInMapper.NewInstance("id", TAXON_NAMESPACE, "parentId", TAXON_NAMESPACE, "accParentId", TAXON_NAMESPACE, null));//there is only one tree
  64                         mapping.addMapper(DbImportSynonymMapper.NewInstance("id", "tu_acctaxon", TAXON_NAMESPACE, null, true));
  65                         mapping.addMapper(DbImportNameTypeDesignationMapper.NewInstance("id", "tu_typetaxon", ErmsTaxonImport.NAME_NAMESPACE, "tu_typedesignationstatus"));
  66 //                      mapping.addMapper(DbNotYetImplementedMapper.NewInstance("tu_acctaxon"));
  67                 }
  68                 return mapping;
  69         }
  70
  71
  72         /* (non-Javadoc)
  73          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.erms.ErmsImportConfigurator)
  74          */
  75         protected String getRecordQuery(ErmsImportConfigurator config) {
  76                 //TODO get automatic by second path mappers
  77                 String selectAttributes = " myTaxon.id, myTaxon.tu_parent, myTaxon.tu_typetaxon, myTaxon.tu_typedesignation, " +
  78                                                                 " myTaxon.tu_acctaxon, myTaxon.tu_status, parent.tu_status AS parentStatus, parent.id AS parentId, " +
  79                                                                 " accParent.tu_status AS accParentStatus, accParent.id AS accParentId ";
  80                 String strRecordQuery =
  81                         " SELECT  " + selectAttributes +
  82                         " FROM tu AS myTaxon LEFT OUTER JOIN " +
  83                                 " tu AS accTaxon ON myTaxon.tu_acctaxon = accTaxon.id LEFT OUTER JOIN " +
  84                                 " tu AS accParent RIGHT OUTER JOIN "  +
  85                                 " tu AS parent ON accParent.id = parent.tu_acctaxon ON myTaxon.tu_parent = parent.id " +
  86                         " WHERE ( myTaxon.id IN (" + ID_LIST_TOKEN + ") )";
  87                 return strRecordQuery;
  88         }
  89
  90
  91         @Override
  92         protected void doInvoke(ErmsImportState state) {
  93                 this.state = state;
  94                 super.doInvoke(state);
  95         }
  96
  97         /* (non-Javadoc)
  98          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
  99          */
 100         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 101                 String nameSpace;
 102                 Class<?> cdmClass;
 103                 Set<String> idSet;
 104                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 105
 106                 try{
 107                         Set<String> taxonIdSet = new HashSet<String>();
 108                         Set<String> nameIdSet = new HashSet<String>();
 109                         while (rs.next()){
 110                                 handleForeignKey(rs, taxonIdSet, "parentId");
 111                                 handleForeignKey(rs, taxonIdSet, "accParentId");
 112                                 handleForeignKey(rs, taxonIdSet, "tu_acctaxon");
 113                                 handleForeignKey(rs, taxonIdSet, "id");
 114                                 handleForeignKey(rs, nameIdSet, "tu_typetaxon");
 115                                 handleForeignKey(rs, nameIdSet, "id");
 116                         }
 117
 118                         //name map
 119                         nameSpace = ErmsTaxonImport.NAME_NAMESPACE;
 120                         cdmClass = TaxonNameBase.class;
 121                         idSet = nameIdSet;
 122                         Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 123                         result.put(nameSpace, nameMap);
 124
 125
 126                         //taxon map
 127                         nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
 128                         cdmClass = TaxonBase.class;
 129                         idSet = taxonIdSet;
 130                         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 131                         result.put(nameSpace, taxonMap);
 132
 133                 } catch (SQLException e) {
 134                         throw new RuntimeException(e);
 135                 }
 136                 return result;
 137         }
 138
 139
 140         /* (non-Javadoc)
 141          * @see eu.etaxonomy.cdm.io.erms.ICheckIgnoreMapper#checkIgnoreMapper(eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper, java.sql.ResultSet)
 142          */
 143         public boolean checkIgnoreMapper(IDbImportMapper mapper, ResultSet rs) throws SQLException{
 144                 boolean result = false;
 145                 if (mapper instanceof DbImportTaxIncludedInMapper){
 146                         //old
 147 //                      int tu_status = rs.getInt("tu_status");
 148 //                      if (tu_status != 1){
 149 //                              result = true;
 150 //                      }
 151
 152                         int id = rs.getInt("id");
 153                         if (state.getAcceptedTaxaKeys().contains(id)){
 154                                 return false;
 155                         }else{
 156                                 return true;
 157                         }
 158                 }else if (mapper instanceof DbImportSynonymMapper){
 159                         //old
 160 //                      int tu_status = rs.getInt("tu_status");
 161 //                      if (tu_status == 1){
 162 //                              result = true;
 163 //                      }else{
 164 //                              return false;
 165 //                      }t.tu_acctaxon <> t.id
 166
 167                         int id = rs.getInt("id");
 168                         Object accTaxonId = rs.getObject("tu_acctaxon");
 169                         if (accTaxonId == null){
 170                                 return true;
 171                         }else{
 172                                 int accId = Integer.valueOf(String.valueOf(accTaxonId));
 173                                 return accId == id;
 174                         }
 175                 }else if (mapper instanceof DbImportNameTypeDesignationMapper){
 176                         Object tu_typeTaxon = rs.getObject("tu_typetaxon");
 177                         if (tu_typeTaxon == null){
 178                                 return true;
 179                         }
 180                 }
 181                 return result;
 182         }
 183
 184         /* (non-Javadoc)
 185          * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
 186          */
 187         public TaxonBase createObject(ResultSet rs, ErmsImportState state) throws SQLException {
 188                 // not needed
 189                 return null;
 190         }
 191
 192
 193
 194         /* (non-Javadoc)
 195          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 196          */
 197         @Override
 198         protected boolean doCheck(ErmsImportState state){
 199 //              IOValidator<ErmsImportState> validator = new ErmsTaxonImportValidator();
 200 //              return validator.validate(state);
 201                 return true;
 202         }
 203
 204
 205         /* (non-Javadoc)
 206          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 207          */
 208         protected boolean isIgnore(ErmsImportState state){
 209                 return ! state.getConfig().isDoRelTaxa();
 210         }
 211
 212
 213
 214 }