app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseSynonymyImport.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2015 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 package eu.etaxonomy.cdm.io.edaphobase;
  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.io.common.IPartitionedIO;
  23 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  24 import eu.etaxonomy.cdm.model.common.CdmBase;
  25 import eu.etaxonomy.cdm.model.reference.Reference;
  26 import eu.etaxonomy.cdm.model.taxon.Synonym;
  27 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  28 import eu.etaxonomy.cdm.model.taxon.Taxon;
  29 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  30
  31 /**
  32  * @author a.mueller
  33  * @date 21.12.2015
  34  *
  35  */
  36 @Component
  37 public class EdaphobaseSynonymyImport extends EdaphobaseImportBase {
  38     private static final long serialVersionUID = 6641343927320994726L;
  39
  40     private static final Logger logger = Logger.getLogger(EdaphobaseSynonymyImport.class);
  41
  42     private static final String tableName = "tax_synonym";
  43
  44     private static final String pluralString = "synonym relationships";
  45
  46
  47     /**
  48      * @param tableName
  49      * @param pluralString
  50      */
  51     public EdaphobaseSynonymyImport() {
  52         super(tableName, pluralString);
  53     }
  54
  55     @Override
  56     protected String getIdQuery(EdaphobaseImportState state) {
  57         return "SELECT tax_synonym_id  "
  58                 + " FROM tax_synonym "
  59                 + " ORDER BY tax_synonym.a_taxon_fk_taxon_id ";
  60     }
  61
  62     @Override
  63     protected String getRecordQuery(EdaphobaseImportConfigurator config) {
  64         String result = "SELECT sr.* "
  65                 + " FROM tax_synonym sr"
  66                 + " WHERE tax_synonym_id IN (@IDSET)";
  67         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  68         return result;
  69     }
  70
  71
  72     @Override
  73     public boolean doPartition(ResultSetPartitioner partitioner, EdaphobaseImportState state) {
  74         ResultSet rs = partitioner.getResultSet();
  75         Map<String, TaxonBase> map = partitioner.getObjectMap(TAXON_NAMESPACE);
  76         Reference<?> sourceReference = state.getTransactionalSourceReference();
  77
  78         Set<TaxonBase> taxaToSave = new HashSet<>();
  79         try {
  80             while (rs.next()){
  81                 int id = rs.getInt("tax_synonym_id");
  82                  //parentTaxonFk
  83 //                boolean isValid = rs.getBoolean("valid");
  84                 Integer synId = nullSafeInt(rs, "a_taxon_fk_taxon_id");
  85                 Integer accId = nullSafeInt(rs, "b_taxon_fk_taxon_id");
  86
  87
  88                 if (synId == null || accId == null){
  89                     logger.warn("Either a_taxon or b_taxon is NULL for tax_synonym " + id);
  90                 }else{
  91                     TaxonBase<?> synonymCandidate = state.getRelatedObject(TAXON_NAMESPACE, String.valueOf(synId), TaxonBase.class);
  92                     if (synonymCandidate == null){
  93                         logger.warn("Synonym " + synId + " not found for synonymRelations (tax_synonym): " + id);
  94                     }else if (synonymCandidate.isInstanceOf(Taxon.class)){
  95                         String message = "Synonym ("+synId+") is not synonym but accepted (valid). Can't add synonym relationship for tax_synonym: "+id;
  96                         logger.warn(message);
  97                     }else{
  98                         Synonym synonym = CdmBase.deproxy(synonymCandidate, Synonym.class);
  99                         TaxonBase<?> accepted = state.getRelatedObject(TAXON_NAMESPACE, String.valueOf(accId), TaxonBase.class);
 100                         if (accepted == null){
 101                             logger.warn("Accepted(parent) taxon " + accId + " not found for tax_synonym " + id );
 102                         }else if(accepted.isInstanceOf(Synonym.class)){
 103                             String message = "Taxon ("+accId+") is not accepted but synonym. Can't add synonym relationship for tax_synonym: "+id;
 104                             logger.warn(message);
 105                         }else{
 106                             Taxon taxon = CdmBase.deproxy(accepted, Taxon.class);
 107                             taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
 108                             taxaToSave.add(synonym);
 109                             taxaToSave.add(taxon);
 110                         }
 111                     }
 112                 }
 113
 114 //              //id
 115 //              String nameSpace = "tax_taxon";
 116 //              ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, nameSpace);
 117 //              ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, nameSpace);
 118
 119
 120             }
 121         } catch (SQLException e) {
 122             // TODO Auto-generated catch block
 123             e.printStackTrace();
 124         }
 125
 126         getTaxonService().saveOrUpdate(taxaToSave);
 127         return true;
 128     }
 129
 130     @Override
 131     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 132             EdaphobaseImportState state) {
 133         String nameSpace;
 134         Class<?> cdmClass;
 135         Set<String> idSet;
 136         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 137
 138         try{
 139             Set<String> taxonIdSet = new HashSet<String>();
 140             while (rs.next()){
 141                 handleForeignKey(rs, taxonIdSet, "a_taxon_fk_taxon_id");
 142                 handleForeignKey(rs, taxonIdSet, "b_taxon_fk_taxon_id");
 143             }
 144
 145             //name map
 146             nameSpace = TAXON_NAMESPACE;
 147             cdmClass = TaxonBase.class;
 148             idSet = taxonIdSet;
 149             Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 150             result.put(nameSpace, taxonMap);
 151
 152         } catch (SQLException e) {
 153             throw new RuntimeException(e);
 154         }
 155
 156         return result;
 157     }
 158
 159
 160     @Override
 161     protected boolean doCheck(EdaphobaseImportState state) {
 162         return false;
 163     }
 164
 165     @Override
 166     protected boolean isIgnore(EdaphobaseImportState state) {
 167         return ! state.getConfig().isDoSynonyms();
 168     }
 169
 170 }