cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonRelationImport.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.pesi.erms;
  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.logging.log4j.LogManager;
  20 import org.apache.logging.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.TaxonName;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  32
  33 /**
  34  * @author a.mueller
  35  * @since 09.03.2010
  36  */
  37 @Component
  38 public class ErmsTaxonRelationImport extends ErmsImportBase<TaxonBase<?>> implements ICheckIgnoreMapper{
  39
  40     private static final long serialVersionUID = 4092728796922591257L;
  41
  42     @SuppressWarnings("unused")
  43     private static Logger logger = LogManager.getLogger();
  44
  45         private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping;
  46
  47         private static final String pluralString = "taxon relations";
  48         private static final String dbTableName = "tu";
  49
  50         private static final Class<?> cdmTargetClass = TaxonBase.class;
  51
  52         @Override
  53     protected int divideCountBy() { return 5;}  //use only 1000 records
  54
  55         public ErmsTaxonRelationImport(){
  56                 super(pluralString, dbTableName, cdmTargetClass);
  57         }
  58
  59         @Override
  60         protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
  61                 if (mapping == null){
  62                         mapping = new DbImportMapping<>();
  63                         //incldued in
  64                         DbImportTaxIncludedInMapper<?> includedIn
  65                             = DbImportTaxIncludedInMapper.NewInstance("id", TAXON_NAMESPACE, "accId", TAXON_NAMESPACE,
  66                                     "parentAccId", TAXON_NAMESPACE, null);
  67                         mapping.addMapper(includedIn);//there is only one tree
  68                         //synonym
  69                         mapping.addMapper(DbImportSynonymMapper.NewInstance("id", "tu_accfinal", TAXON_NAMESPACE,
  70                                 "tu_unacceptreason", null, null, true));
  71                         //type designations
  72                         mapping.addMapper(DbImportNameTypeDesignationMapper.NewInstance("id", "tu_typetaxon", ErmsImportBase.NAME_NAMESPACE, "tu_typedesignationstatus"));
  73                 }
  74                 return mapping;
  75         }
  76
  77     @Override
  78     protected String getIdQuery(){
  79         String result = " SELECT id FROM " + getTableName() +
  80                 " ORDER BY tu_sp";
  81         return result;
  82     }
  83
  84     @Override
  85     protected String getRecordQuery(ErmsImportConfigurator config) {
  86                 //TODO get automatic by second path mappers
  87                 String selectAttributes =
  88                     "   myTaxon.id, myTaxon.tu_parent, myTaxon.tu_typetaxon, myTaxon.tu_typedesignation, "
  89                     + " myTaxon.tu_accfinal, myTaxon.tu_status, myTaxon.tu_unacceptreason, "
  90                         + " parent.tu_status AS parentStatus, parent.id AS parentId, "
  91                     + " parentAcc.id AS parentAccId,"
  92                     + " accTaxon.tu_parent accParentId, "
  93                     + " CASE WHEN myTaxon.id = parentAcc.id THEN parent.id ELSE ISNULL(parentAcc.id, parent.id) END as accId ";
  94                 String strRecordQuery =
  95                         "   SELECT  " + selectAttributes
  96                         + " FROM tu AS myTaxon "
  97                         + "   LEFT JOIN tu AS accTaxon ON myTaxon.tu_accfinal = accTaxon.id "
  98                         + "   LEFT JOIN tu AS parent ON myTaxon.tu_parent = parent.id "
  99                         + "   LEFT JOIN tu AS parentAcc ON parentAcc.id = parent.tu_accfinal "
 100                         + " WHERE ( myTaxon.id IN (" + ID_LIST_TOKEN + ") )";
 101                 return strRecordQuery;
 102         }
 103
 104         @Override
 105         protected void doInvoke(ErmsImportState state) {
 106                 super.doInvoke(state);
 107         }
 108
 109         @Override
 110         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, ErmsImportState state) {
 111
 112             String nameSpace;
 113                 Set<String> idSet;
 114                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 115
 116                 try{
 117                         Set<String> taxonIdSet = new HashSet<>();
 118                         Set<String> nameIdSet = new HashSet<>();
 119                         while (rs.next()){
 120                             handleForeignKey(rs, taxonIdSet, "accId");
 121                                 handleForeignKey(rs, taxonIdSet, "tu_accfinal");
 122                                 handleForeignKey(rs, taxonIdSet, "id");
 123                                 handleForeignKey(rs, nameIdSet, "tu_typetaxon");
 124                                 handleForeignKey(rs, nameIdSet, "id");
 125                         }
 126
 127                         //name map
 128                         nameSpace = ErmsImportBase.NAME_NAMESPACE;
 129                         idSet = nameIdSet;
 130                         Map<String, TaxonName> nameMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
 131                         result.put(nameSpace, nameMap);
 132
 133                         //taxon map
 134                         nameSpace = ErmsImportBase.TAXON_NAMESPACE;
 135                         idSet = taxonIdSet;
 136                         @SuppressWarnings("rawtypes")
 137             Map<String, TaxonBase> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace);
 138                         result.put(nameSpace, taxonMap);
 139
 140                         return result;
 141
 142                 } catch (SQLException e) {
 143                         throw new RuntimeException(e);
 144                 }
 145         }
 146
 147         @Override
 148     public boolean checkIgnoreMapper(@SuppressWarnings("rawtypes") IDbImportMapper mapper, ResultSet rs) throws SQLException{
 149
 150             boolean result = false;
 151         boolean isAccepted = isAccepted(rs);
 152
 153         if (mapper instanceof DbImportTaxIncludedInMapper){
 154                     //here we should add the direct parent or the accepted taxon of the parent
 155                     return !isAccepted;
 156                 }else if (mapper instanceof DbImportSynonymMapper){
 157                 //the only exact rule in ERMS is that the accepted taxon (tu_accfinal)
 158                 // of a synonym (def: id <> tu_accfinal) never again has another
 159                 // accepted taxon.
 160                 //So the synonym relation is clearly defined, no matter which status
 161                 //both related taxa have.
 162                 //TODO: check if data were only adapted by BGBM this way
 163                         return isAccepted;
 164                 }else if (mapper instanceof DbImportNameTypeDesignationMapper){
 165                         Object tu_typeTaxon = rs.getObject("tu_typetaxon");
 166                         if (tu_typeTaxon == null){
 167                                 return true;
 168                         }
 169                 }
 170                 return result;
 171         }
 172
 173     private boolean isAccepted(ResultSet rs) throws SQLException {
 174         int id = rs.getInt("id");
 175         Object accTaxonId = rs.getObject("tu_accfinal");
 176         Object accParentId = rs.getObject("accParentId");
 177
 178         boolean isAccepted = false;
 179         if(accTaxonId == null){
 180             isAccepted = true;  //if accTaxonId == null we can only assume this taxon is accepted as we have no other accepted taxon, though in most cases the status is not accepted
 181         }else if (id == (int)accTaxonId){
 182             isAccepted = true;
 183         }else if (accParentId != null && id == (int)accParentId){
 184             //see also ErmsTaxonImport.getAcceptedTaxaKeys, there with accepted taxon (alternate representation) being there own child. These should be fully accepted as other wise the link to the higher taxon (genus) is not given
 185             isAccepted = true;
 186         }
 187         return isAccepted;
 188     }
 189
 190         @Override
 191         protected boolean doCheck(ErmsImportState state){
 192 //              IOValidator<ErmsImportState> validator = new ErmsTaxonImportValidator();
 193 //              return validator.validate(state);
 194                 return true;
 195         }
 196
 197         @Override
 198         protected boolean isIgnore(ErmsImportState state){
 199                 return ! state.getConfig().isDoRelTaxa();
 200         }
 201 }