app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraImportBase.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.Map;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.common.CdmUtils;
  18 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  19 import eu.etaxonomy.cdm.io.common.DbImportBase;
  20 import eu.etaxonomy.cdm.io.common.ICdmIO;
  21 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  22 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  23 import eu.etaxonomy.cdm.model.reference.ISourceable;
  24 import eu.etaxonomy.cdm.model.reference.Reference;
  25 import eu.etaxonomy.cdm.model.taxon.Taxon;
  26 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  27
  28 /**
  29  * @author a.mueller
  30  * @since 20.03.2008
  31  */
  32 public abstract class MexicoEfloraImportBase
  33             extends DbImportBase<MexicoEfloraImportState, MexicoEfloraImportConfigurator>
  34             implements ICdmIO<MexicoEfloraImportState>, IPartitionedIO<MexicoEfloraImportState> {
  35
  36     private static final long serialVersionUID = -5229728676004248450L;
  37     private static final Logger logger = Logger.getLogger(MexicoEfloraImportBase.class);
  38
  39         public MexicoEfloraImportBase(String tableName, String pluralString ) {
  40                 super(tableName, pluralString);
  41         }
  42
  43         @Override
  44     protected String getIdQuery(MexicoEfloraImportState state){
  45                 String result = " SELECT " + getTableName() + "id FROM " + getTableName();
  46                 return result;
  47         }
  48
  49     //can be overriden
  50     protected String getIdInSource(MexicoEfloraImportState state, ResultSet rs) throws SQLException {
  51         return null;
  52     }
  53
  54
  55         protected Taxon getTaxon(BerlinModelImportState state, int taxonId, Map<String, TaxonBase> taxonMap, int factId) {
  56                 TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));
  57
  58                 //TODO for testing
  59 //              if (taxonBase == null && ! state.getConfig().isDoTaxa()){
  60 //                      taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
  61 //              }
  62
  63                 Taxon taxon;
  64                 if ( taxonBase instanceof Taxon ) {
  65                         taxon = (Taxon) taxonBase;
  66                 } else if (taxonBase != null) {
  67                         logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
  68                         return null;
  69                 } else {
  70                         logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " is null.");
  71                         return null;
  72                 }
  73                 return taxon;
  74         }
  75
  76
  77         /**
  78          *      Searches first in the detail maps then in the ref maps for a reference.
  79          *  Returns the reference as soon as it finds it in one of the map, according
  80          *  to the order of the map.
  81          *  If nomRefDetailFk is <code>null</code> no search on detail maps is performed.
  82          *  If one of the maps is <code>null</code> no search on the according map is
  83          *  performed. <BR>
  84          *  You may define the order of search by the order you pass the maps but
  85          *  make sure to always pass the detail maps first.
  86          * @param firstDetailMap
  87          * @param secondDetailMap
  88          * @param firstRefMap
  89          * @param secondRefMap
  90          * @param nomRefDetailFk
  91          * @param nomRefFk
  92          * @return
  93          */
  94         protected Reference getReferenceFromMaps(
  95                         Map<String, Reference> detailMap,
  96                         Map<String, Reference> refMap,
  97                         String nomRefDetailFk,
  98                         String nomRefFk) {
  99                 Reference ref = null;
 100                 if (detailMap != null){
 101                         ref = detailMap.get(nomRefDetailFk);
 102                 }
 103                 if (ref == null){
 104                         ref = refMap.get(nomRefFk);
 105                 }
 106                 return ref;
 107         }
 108
 109     protected Reference getSourceReference(Reference sourceReference) {
 110         Reference persistentSourceReference = getReferenceService().find(sourceReference.getUuid());  //just to be sure
 111         if (persistentSourceReference != null){
 112             sourceReference = persistentSourceReference;
 113         }
 114         return sourceReference;
 115     }
 116
 117     protected static <T extends IdentifiableSource> boolean importSourceExists(ISourceable<T> sourceable, String idInSource,
 118             String namespace, Reference ref) {
 119         for (T source : sourceable.getSources()){
 120             if (CdmUtils.nullSafeEqual(namespace, source.getIdNamespace()) &&
 121                 CdmUtils.nullSafeEqual(idInSource, source.getIdInSource()) &&
 122                 CdmUtils.nullSafeEqual(ref, source.getCitation())){
 123                     return true;
 124             }
 125         }
 126         return false;
 127     }
 128 }