app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraCommonNameRefImport.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 package eu.etaxonomy.cdm.io.mexico;
  10
  11 import java.sql.ResultSet;
  12 import java.sql.SQLException;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  24 import eu.etaxonomy.cdm.model.common.CdmBase;
  25 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  26 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  27 import eu.etaxonomy.cdm.model.name.TaxonName;
  28 import eu.etaxonomy.cdm.model.reference.Reference;
  29
  30 /**
  31  * @author a.mueller
  32  * @since 08.02.2022
  33  */
  34 @Component
  35 public class MexicoEfloraCommonNameRefImport extends MexicoEfloraImportBase {
  36
  37     private static final long serialVersionUID = -1712022169834400067L;
  38     private static final Logger logger = Logger.getLogger(MexicoEfloraCommonNameRefImport.class);
  39
  40         protected static final String NAMESPACE = "CommonNameRef";
  41
  42         private static final String pluralString = "common name sources";
  43         private static final String dbTableName = "Eflora_RelBiblioNomComun";
  44
  45         public MexicoEfloraCommonNameRefImport(){
  46                 super(dbTableName, pluralString);
  47         }
  48
  49         @Override
  50         protected String getIdQuery(MexicoEfloraImportState state) {
  51                 String sql = " SELECT IdCombinado "
  52                         + " FROM " + dbTableName
  53                         + " ORDER BY IdCombinado ";
  54                 return sql;
  55         }
  56
  57         @Override
  58         protected String getRecordQuery(MexicoEfloraImportConfigurator config) {
  59                 String sqlSelect = " SELECT * ";
  60                 String sqlFrom = " FROM " + dbTableName;
  61                 String sqlWhere = " WHERE ( IdCombinado IN (" + ID_LIST_TOKEN + ") )";
  62
  63                 String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere ;
  64                 return strRecordQuery;
  65         }
  66
  67         @Override
  68         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, MexicoEfloraImportState state) {
  69
  70             boolean success = true ;
  71
  72             @SuppressWarnings("unchecked")
  73         Map<String, CommonTaxonName> commonNameMap = partitioner.getObjectMap(MexicoEfloraCommonNameImport.NAMESPACE);
  74
  75             @SuppressWarnings("unchecked")
  76             Map<String, Reference> referenceMap = partitioner.getObjectMap(MexicoEfloraReferenceImportBase.NAMESPACE);
  77
  78                 ResultSet rs = partitioner.getResultSet();
  79                 try{
  80                         while (rs.next()){
  81
  82                         //      if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
  83
  84                                 //create TaxonName element
  85                                 String idCombi = rs.getString("IdCombinado");
  86                                 int idBibliografia = rs.getInt("IdBibliografia");
  87                                 String observaciones = rs.getString("Observaciones");
  88                                 //needed?
  89 //                              String idNomComun = rs.getString("IdNomComun");
  90
  91                             try {
  92                                 CommonTaxonName commonName = commonNameMap.get(idCombi);
  93
  94                                 Reference ref = referenceMap.get(String.valueOf(idBibliografia));
  95 //                              String detail = state.getRefDetailMap().get(idBibliografia);
  96                                 String detail = null;
  97
  98                                 if (commonName != null) {
  99                                     DescriptionElementSource source = commonName.addPrimaryTaxonomicSource(ref, detail);
 100                                     if (source!= null) {
 101                                         TaxonName nameUsedInSource = getNameUsedInSource(state, observaciones);
 102                                         source.setNameUsedInSource(nameUsedInSource);
 103                                         //TODO other observaciones
 104                                     } else {
 105                                         logger.warn("Source not found for " + idCombi + " and bibID: " + idBibliografia);
 106                                     }
 107                                 }else {
 108                                     logger.warn("CommonName not found for " + idCombi);
 109                                 }
 110
 111                                         partitioner.startDoSave();
 112                                 } catch (Exception e) {
 113                                     e.printStackTrace();
 114                                         logger.warn("An exception (" +e.getMessage()+") occurred when trying to create common name for id " + idCombi + ".");
 115                                         success = false;
 116                                 }
 117                         }
 118                 } catch (Exception e) {
 119                         logger.error("SQLException:" +  e);
 120                         return false;
 121                 }
 122
 123                 logger.warn("Finished partition");
 124
 125                 return success;
 126         }
 127
 128     private TaxonName getNameUsedInSource(MexicoEfloraImportState state, String observaciones) {
 129         // TODO named used in source for common names
 130         return null;
 131     }
 132
 133     @Override
 134         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, MexicoEfloraImportState state) {
 135
 136         String nameSpace;
 137                 Set<String> idSet;
 138                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 139
 140                 try{
 141                         Set<String> commonNameIdSet = new HashSet<>();
 142             Set<String> referenceIdSet = new HashSet<>();
 143             while (rs.next()){
 144                 handleForeignKey(rs, referenceIdSet, "IdBibliografia");
 145                 handleForeignKey(rs, commonNameIdSet, "IdCombinado");
 146             }
 147
 148                         //common name map
 149                         nameSpace = MexicoEfloraCommonNameImport.NAMESPACE;
 150                         Map<UUID,String> uuidMap = new HashMap<>();
 151                         commonNameIdSet.stream().forEach(cnId->uuidMap.put(state.getCommonNameMap().get(cnId),cnId));
 152                         @SuppressWarnings({ "rawtypes", "unchecked" })
 153             List<CommonTaxonName> commonNames = (List)getDescriptionElementService().find(uuidMap.keySet());
 154                         Map<String, CommonTaxonName> commonNameMap = new HashMap<>();
 155                         commonNames.stream().forEach(cn->commonNameMap.put(uuidMap.get(cn.getUuid()), cn));
 156                         result.put(nameSpace, commonNameMap);
 157
 158             //reference map
 159             nameSpace = MexicoEfloraReferenceImportBase.NAMESPACE;
 160             idSet = referenceIdSet;
 161             Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 162             result.put(nameSpace, referenceMap);
 163
 164                 } catch (SQLException e) {
 165                         throw new RuntimeException(e);
 166                 }
 167                 return result;
 168         }
 169
 170         @Override
 171         protected String getTableName() {
 172                 return dbTableName;
 173         }
 174
 175         @Override
 176         public String getPluralString() {
 177                 return pluralString;
 178         }
 179
 180     @Override
 181     protected boolean doCheck(MexicoEfloraImportState state){
 182         return true;
 183     }
 184
 185         @Override
 186         protected boolean isIgnore(MexicoEfloraImportState state){
 187                 return ! state.getConfig().isDoTaxa();
 188         }
 189 }