app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraPictureImport.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
  10 package eu.etaxonomy.cdm.io.algaterra;
  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.algaterra.validation.AlgaTerraTypeImportValidator;
  23 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  25 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;
  26 import eu.etaxonomy.cdm.io.common.IOValidator;
  27 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.media.Media;
  30 import eu.etaxonomy.cdm.model.taxon.Taxon;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  32
  33
  34 /**
  35  * Import for AlgaTerra images from table
  36  * @author a.mueller
  37  * @created 18.01.2013
  38  */
  39 @Component
  40 public class AlgaTerraPictureImport  extends AlgaTerraImageImportBase {
  41         private static final Logger logger = Logger.getLogger(AlgaTerraPictureImport.class);
  42
  43
  44         private static int modCount = 5000;
  45         private static final String pluralString = "pictures";
  46         private static final String dbTableName = "Picture";  //??
  47
  48         public AlgaTerraPictureImport(){
  49                 super(dbTableName, pluralString);
  50         }
  51
  52
  53         /* (non-Javadoc)
  54          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  55          */
  56         @Override
  57         protected String getIdQuery(BerlinModelImportState state) {
  58                 String result = " SELECT p.PictureId "
  59                                 + " FROM Picture p  INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk "
  60                                 + " WHERE f.FactCategoryFk = 205 "
  61                                 + " ORDER BY p.PictureId ";
  62                 return result;
  63         }
  64
  65         /* (non-Javadoc)
  66          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  67          */
  68         @Override
  69         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  70                         String strQuery =
  71
  72                                 " SELECT p.*, f.*, pt.RIdentifier, p.PicturePhrase as FigurePhrase, p.PictureFile as fileName, p.PicturePath as filePath " +
  73                     " FROM Picture p INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk "
  74                     +   " WHERE f.FactCategoryFk = 205 AND ( p.PictureID IN (" + ID_LIST_TOKEN + ")     )"
  75                     + " ORDER BY p.PictureId, f.factId, pt.RIdentifier ";
  76             ;
  77                 return strQuery;
  78         }
  79
  80         /* (non-Javadoc)
  81          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
  82          */
  83         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
  84                 boolean success = true;
  85
  86                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
  87
  88 //              Set<SpecimenOrObservationBase> specimenToSave = new HashSet<SpecimenOrObservationBase>();
  89                 Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
  90
  91 //              Map<String, DerivedUnitBase> ecoFactMap = (Map<String, DerivedUnitBase>) partitioner.getObjectMap(AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE);
  92                 Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
  93
  94                 ResultSet rs = partitioner.getResultSet();
  95
  96                 try {
  97
  98                         int i = 0;
  99
 100                         //for each reference
 101             while (rs.next()){
 102
 103                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 104
 105                                 int pictureId = rs.getInt("PictureID");
 106                                 int taxonId = rs.getInt("RIdentifier");
 107                                 int factId = rs.getInt("FactId");
 108
 109
 110                                 //TODO etc. Created, Notes, Copyright, TermsOfUse etc.
 111
 112                                 try {
 113
 114                                         TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));
 115                                         if (taxonBase == null){
 116                                                 logger.warn("Could not find taxon (" + taxonId +") for picture fact " +  factId);
 117                                         }else if (! taxonBase.isInstanceOf(Taxon.class)){
 118                                                 logger.warn("Taxon is not of class Taxon but " + taxonBase.getClass() + ". RIdentifier: " + taxonId + " PictureId: " +  pictureId + ", FactId: "+  factId);
 119
 120                                         }else{
 121                                                 Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 122
 123                                                 Media media = handleSingleImage(rs, taxon, state, partitioner);
 124
 125                                                 handlePictureSpecificFields(rs, media, state);
 126
 127                                                 taxaToSave.add(taxon);
 128                                         }
 129
 130
 131                                 } catch (Exception e) {
 132                                         logger.warn("Exception in " + getTableName() + ": PictureId " + pictureId + ". " + e.getMessage());
 133                                         e.printStackTrace();
 134                                 }
 135
 136             }
 137
 138 //            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
 139
 140                         logger.warn(pluralString + " to save: " + taxaToSave.size());
 141 //                      getOccurrenceService().save(taxaToSave);
 142                         getTaxonService().save(taxaToSave);
 143
 144                         return success;
 145                 } catch (SQLException e) {
 146                         logger.error("SQLException:" +  e);
 147                         return false;
 148                 }
 149         }
 150
 151
 152
 153         private void handlePictureSpecificFields(ResultSet rs, Media media, AlgaTerraImportState state) throws SQLException {
 154                 //TODO
 155
 156         }
 157
 158
 159         /* (non-Javadoc)
 160          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 161          */
 162         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 163                 String nameSpace;
 164                 Class cdmClass;
 165                 Set<String> idSet;
 166                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 167
 168                 try{
 169                         Set<String> taxonIdSet = new HashSet<String>();
 170
 171                         while (rs.next()){
 172                                 handleForeignKey(rs, taxonIdSet, "RIdentifier");
 173                         }
 174
 175                         //taxon map
 176                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 177                         cdmClass = TaxonBase.class;
 178                         idSet = taxonIdSet;
 179                         Map<String, TaxonBase> taxonMap = (Map<String,TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 180                         result.put(nameSpace, taxonMap);
 181
 182
 183                 } catch (SQLException e) {
 184                         throw new RuntimeException(e);
 185                 }
 186                 return result;
 187         }
 188
 189
 190
 191
 192         /* (non-Javadoc)
 193          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 194          */
 195         @Override
 196         protected boolean doCheck(BerlinModelImportState state){
 197                 IOValidator<BerlinModelImportState> validator = new AlgaTerraTypeImportValidator();
 198                 return validator.validate(state);
 199         }
 200
 201         /* (non-Javadoc)
 202          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 203          */
 204         protected boolean isIgnore(BerlinModelImportState bmState){
 205                 AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator();
 206 //              return !  ( config.isDoTypes() && config.isDoImages()) ;
 207                 return false;
 208         }
 209
 210 }