app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraFactImport.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.CategoricalData;
  26 import eu.etaxonomy.cdm.model.description.Feature;
  27 import eu.etaxonomy.cdm.model.description.State;
  28 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  29 import eu.etaxonomy.cdm.model.reference.Reference;
  30 import eu.etaxonomy.cdm.model.taxon.Taxon;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  32
  33 /**
  34  * @author a.mueller
  35  * @since 08.02.2022
  36  */
  37 @Component
  38 public class MexicoEfloraFactImport extends MexicoEfloraImportBase {
  39
  40     private static final long serialVersionUID = 8097679811768529307L;
  41     private static final Logger logger = Logger.getLogger(MexicoEfloraFactImport.class);
  42
  43         protected static final String NAMESPACE = "Facts";
  44
  45         private static final String pluralString = "facts";
  46         private static final String dbTableName = "Eflora_RelBiblioNombreCatalogoNombre";
  47
  48         public MexicoEfloraFactImport(){
  49                 super(dbTableName, pluralString);
  50         }
  51
  52         @Override
  53         protected String getIdQuery(MexicoEfloraImportState state) {
  54                 String sql = " SELECT id  "
  55                         + " FROM " + dbTableName
  56                         + " ORDER BY IdCAT, IdCatNombre, IdBibliografia ";
  57                 return sql;
  58         }
  59
  60         @Override
  61         protected String getRecordQuery(MexicoEfloraImportConfigurator config) {
  62                 String sqlSelect = " SELECT f.*, t.uuid taxonUuid ";
  63                 String sqlFrom = " FROM " + dbTableName + " f LEFT JOIN " + MexicoEfloraTaxonImport.dbTableName + " t ON f.IdCAT = t.IdCAT ";
  64                 String sqlWhere = " WHERE ( Id IN (" + ID_LIST_TOKEN + ") )";
  65                 String sqlOrderBy = " ORDER BY IdCAT, IdCatNombre, IdBibliografia";
  66
  67                 String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere + sqlOrderBy;
  68                 return strRecordQuery;
  69         }
  70
  71         private CategoricalData lastFact;
  72         private String lastIdCat = "-1";
  73         private int lastIdCatNombre = -1;
  74         @Override
  75         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, MexicoEfloraImportState state) {
  76
  77             Reference sourceReference = this.getSourceReference(state.getConfig().getSourceReference());
  78             //hope this is transaction save
  79             if (lastFact != null) {
  80                 lastFact = (CategoricalData)getDescriptionElementService().find(lastFact.getUuid());
  81             }
  82             boolean success = true ;
  83
  84             @SuppressWarnings("unchecked")
  85         Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(MexicoEfloraTaxonImport.NAMESPACE);
  86         @SuppressWarnings("unchecked")
  87         Map<String, Reference> referenceMap = partitioner.getObjectMap(MexicoEfloraReferenceImportBase.NAMESPACE);
  88
  89                 ResultSet rs = partitioner.getResultSet();
  90                 try{
  91                         while (rs.next()){
  92
  93                         //      if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
  94
  95                                 //create TaxonName element
  96                             int id = rs.getInt("id");  //only for partitioning and logging
  97                                 String idCAT = rs.getString("IdCAT");
  98                                 int idCatNombre = rs.getInt("IdCatNombre");
  99                                 String uuidTaxonStr = rs.getString("taxonUuid");
 100
 101                 int idBibliografia = rs.getInt("IdBibliografia");
 102                 //TODO observaciones in facts
 103                 String observaciones = rs.getString("Observaciones");
 104
 105                             try {
 106                                 CategoricalData categoricalData;
 107                                 if (idCAT.equals(lastIdCat) && idCatNombre == lastIdCatNombre) {
 108                                     categoricalData = lastFact;
 109                                 }else {
 110                                     categoricalData = makeCategoricalData(state, idCatNombre);
 111                                     Feature lastFeature = lastFact == null? null : lastFact.getFeature();
 112                         if (idCAT.equals(lastIdCat) && categoricalData.getFeature().equals(lastFeature)) {
 113                             //merge
 114                             //add the single new state to the existing categorical data
 115                             //TODO not fully correct if bibliography differs for the single states;
 116                             State newState = categoricalData.getStatesOnly().stream().findFirst().orElse(null);
 117                             if (newState != null) {
 118                                 lastFact.addStateData(newState);
 119                             }
 120                             categoricalData  = lastFact;
 121 //                            lastIdCatNombre = idCatNombre;
 122                         }else {
 123                             //new categorical data
 124                             TaxonBase<?> taxonBase = taxonMap.get(uuidTaxonStr);
 125                             Taxon taxon;
 126                             if (taxonBase.isInstanceOf(Taxon.class)) {
 127                                 taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 128                             }else {
 129                                 logger.warn(idCatNombre + ": Taxon is not accepted: " + idCAT);
 130                                 continue;
 131                             }
 132
 133                             //TODO source reference correct?
 134                             TaxonDescription description = this.getTaxonDescription(taxon, sourceReference,
 135                                     false, true);
 136                             description.addElement(categoricalData);
 137                             lastFact = categoricalData;
 138                             lastIdCat = idCAT;
 139                             lastIdCatNombre = idCatNombre;
 140                         }
 141                                 }
 142                                 handleBibliografia(state, referenceMap, categoricalData, idBibliografia, id);
 143
 144                                         partitioner.startDoSave();
 145                                 } catch (Exception e) {
 146                                     e.printStackTrace();
 147                                         logger.warn("An exception (" +e.getMessage()+") occurred when trying to create fact for id " + id + ".");
 148                                         success = false;
 149                                 }
 150                         }
 151                 } catch (Exception e) {
 152                         logger.error("SQLException:" +  e);
 153                         return false;
 154                 }
 155             logger.warn("Next partition");
 156
 157                 return success;
 158         }
 159
 160     private void handleBibliografia(MexicoEfloraImportState state, Map<String, Reference> referenceMap,
 161             CategoricalData categoricalData, int idBibliografia,
 162             int id) {
 163         Reference ref = referenceMap == null ? null : referenceMap.get(String.valueOf(idBibliografia));
 164 //        String detail = state.getRefDetailMap().get(idBibliografia);
 165         String detail = null;
 166
 167         if (ref != null) {
 168             if (categoricalData != null) {
 169                 categoricalData.addPrimaryTaxonomicSource(ref, detail);
 170             }else {
 171                 logger.warn("Fact does not exist: " + id);
 172             }
 173         }else {
 174             logger.warn("Source not found for " + id + " and bibID: " + idBibliografia);
 175         }
 176     }
 177
 178     private CategoricalData makeCategoricalData(MexicoEfloraImportState importState,
 179             int idCatNombre) {
 180         Feature feature = getFeature(importState, idCatNombre);
 181         State state = getState(importState, idCatNombre);
 182         CategoricalData categoricalData = CategoricalData.NewInstance(state, feature);
 183         return categoricalData;
 184     }
 185
 186     private State getState(MexicoEfloraImportState importState, int idCatNombre) {
 187         State result = importState.getStateMap().get(idCatNombre);
 188         if (result == null) {
 189             logger.warn("State does not exist: " + idCatNombre);
 190         }
 191         return result;
 192     }
 193
 194     private Feature getFeature(MexicoEfloraImportState importState, int idCatNombre) {
 195         return importState.getFeatureMap().get(idCatNombre);
 196     }
 197
 198     @Override
 199         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, MexicoEfloraImportState state) {
 200
 201         String nameSpace;
 202                 Set<String> idSet;
 203                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 204
 205                 try{
 206                         Set<UUID> taxonIdSet = new HashSet<>();
 207                         Set<String> referenceIdSet = new HashSet<>();
 208                         while (rs.next()){
 209                                 handleForeignUuidKey(rs, taxonIdSet, "taxonUuid");
 210                                 handleForeignKey(rs, referenceIdSet, "IdBibliografia");
 211                         }
 212
 213                         //taxon map
 214                         nameSpace = MexicoEfloraTaxonImport.NAMESPACE;
 215                         @SuppressWarnings("rawtypes")
 216             Map<String, TaxonBase> taxonMap = new HashMap<>();
 217                         @SuppressWarnings("rawtypes")
 218             List<TaxonBase> taxa = getTaxonService().find(taxonIdSet);
 219                         taxa.stream().forEach(t->taxonMap.put(t.getUuid().toString(), t));
 220                         result.put(nameSpace, taxonMap);
 221
 222                         //reference map
 223                         nameSpace = MexicoEfloraReferenceImportBase.NAMESPACE;
 224                         idSet = referenceIdSet;
 225                         Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 226                         result.put(nameSpace, referenceMap);
 227
 228                 } catch (SQLException e) {
 229                         throw new RuntimeException(e);
 230                 }
 231                 return result;
 232         }
 233
 234         @Override
 235         protected String getTableName() {
 236                 return dbTableName;
 237         }
 238
 239         @Override
 240         public String getPluralString() {
 241                 return pluralString;
 242         }
 243
 244     @Override
 245     protected boolean doCheck(MexicoEfloraImportState state){
 246         return true;
 247     }
 248
 249         @Override
 250         protected boolean isIgnore(MexicoEfloraImportState state){
 251                 return ! state.getConfig().isDoTaxa();
 252         }
 253 }