app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraDistributionRefImport.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.DescriptionElementSource;
  26 import eu.etaxonomy.cdm.model.description.Distribution;
  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 MexicoEfloraDistributionRefImport extends MexicoEfloraImportBase {
  36
  37     private static final long serialVersionUID = -3358763003286536675L;
  38     private static final Logger logger = Logger.getLogger(MexicoEfloraDistributionRefImport.class);
  39
  40         protected static final String NAMESPACE = "DistributionRef";
  41
  42         private static final String pluralString = "distribution sources";
  43         private static final String dbTableName = "Eflora_RelRegionBibliografia";
  44
  45         public MexicoEfloraDistributionRefImport(){
  46                 super(dbTableName, pluralString);
  47         }
  48
  49         @Override
  50         protected String getIdQuery(MexicoEfloraImportState state) {
  51                 String sql = " SELECT IdDist "
  52                         + " FROM " + dbTableName
  53                         + " ORDER BY IdDist ";
  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 ( IdDist 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, Distribution> distributionMap = partitioner.getObjectMap(MexicoEfloraDistributionImport.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("IdDist");
  86                                 int idBibliografia = rs.getInt("IdBibliografia");
  87                             String observaciones = rs.getString("Observaciones");
  88
  89                             try {
  90                                 Distribution distribution = distributionMap.get(idCombi);
  91                                 if (distribution == null) {
  92                                     logger.warn("Distribution not found for " + idCombi);
  93                                     continue;
  94                                 }
  95                                 Reference ref = referenceMap.get(String.valueOf(idBibliografia));
  96                                 String detail = state.getRefDetailMap().get(idBibliografia);
  97
  98
  99                                 DescriptionElementSource source = distribution.addPrimaryTaxonomicSource(ref, detail);
 100                     //TODO nameUsedInSource for distribution
 101                     if (source!= null) {
 102                         TaxonName nameUsedInSource = getNameUsedInSource(state, observaciones);
 103                         source.setNameUsedInSource(nameUsedInSource);
 104                         //TODO other observaciones
 105                     } else {
 106                         logger.warn("Source not found for " + idCombi + " and bibID: " + idBibliografia);
 107                     }
 108
 109                                         partitioner.startDoSave();
 110 //                                      taxaToSave.add(taxonBase);
 111                                 } catch (Exception e) {
 112                                     e.printStackTrace();
 113                                         logger.warn("An exception (" +e.getMessage()+") occurred when trying to create common name for id " + idCombi + ".");
 114                                         success = false;
 115                                 }
 116                         }
 117                 } catch (Exception e) {
 118                         logger.error("SQLException:" +  e);
 119                         return false;
 120                 }
 121
 122                 logger.warn("Partition finished");
 123                 return success;
 124         }
 125
 126     private TaxonName getNameUsedInSource(MexicoEfloraImportState state, String observaciones) {
 127         // TODO Auto-generated method stub
 128         return null;
 129     }
 130
 131     @Override
 132         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, MexicoEfloraImportState state) {
 133
 134         String nameSpace;
 135                 Set<String> idSet;
 136                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 137
 138                 try{
 139                         Set<String> distributionIdSet = new HashSet<>();
 140                         Set<String> referenceIdSet = new HashSet<>();
 141                         while (rs.next()){
 142                             handleForeignKey(rs, referenceIdSet, "IdBibliografia");
 143                 handleForeignKey(rs,distributionIdSet, "IdDist");
 144                         }
 145
 146             //distribution map
 147             nameSpace = MexicoEfloraDistributionImport.NAMESPACE;
 148             Map<UUID,String> uuidMap = new HashMap<>();
 149             distributionIdSet.stream().forEach(dId->uuidMap.put(state.getDistributionMap().get(dId),dId));
 150             @SuppressWarnings({ "rawtypes", "unchecked" })
 151             List<Distribution> distributions = (List)getDescriptionElementService().find(uuidMap.keySet());
 152             Map<String, Distribution> distributionMap = new HashMap<>();
 153             distributions.stream().forEach(d->distributionMap.put(uuidMap.get(d.getUuid()), d));
 154             result.put(nameSpace, distributionMap);
 155
 156             //reference map
 157             nameSpace = MexicoEfloraReferenceImportBase.NAMESPACE;
 158             idSet = referenceIdSet;
 159             Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 160             result.put(nameSpace, referenceMap);
 161
 162                 } catch (SQLException e) {
 163                         throw new RuntimeException(e);
 164                 }
 165                 return result;
 166         }
 167
 168         @Override
 169         protected String getTableName() {
 170                 return dbTableName;
 171         }
 172
 173         @Override
 174         public String getPluralString() {
 175                 return pluralString;
 176         }
 177
 178     @Override
 179     protected boolean doCheck(MexicoEfloraImportState state){
 180         return true;
 181     }
 182
 183         @Override
 184         protected boolean isIgnore(MexicoEfloraImportState state){
 185                 return ! state.getConfig().isDoTaxa();
 186         }
 187 }