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.api.facade.DerivedUnitFacade;
  23 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  24 import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraTypeImportValidator;
  25 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  26 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  27 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;
  28 import eu.etaxonomy.cdm.io.common.IOValidator;
  29 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.media.Media;
  32 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  33 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  34 import eu.etaxonomy.cdm.model.taxon.Taxon;
  35 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  36
  37
  38 /**
  39  * Import for AlgaTerra images from table
  40  * @author a.mueller
  41  * @created 18.01.2013
  42  */
  43 @Component
  44 public class AlgaTerraPictureImport  extends AlgaTerraImageImportBase {
  45         private static final Logger logger = Logger.getLogger(AlgaTerraPictureImport.class);
  46
  47
  48         private static int modCount = 5000;
  49         private static final String pluralString = "pictures";
  50         private static final String dbTableName = "Picture";  //??
  51
  52         public AlgaTerraPictureImport(){
  53                 super(dbTableName, pluralString);
  54         }
  55
  56
  57         /* (non-Javadoc)
  58          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  59          */
  60         @Override
  61         protected String getIdQuery(BerlinModelImportState state) {
  62                 String result = " SELECT p.PictureId "
  63                                 + " 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 "
  64                                 + " WHERE f.FactCategoryFk = 205 AND p.RestrictedFlag = 0 "
  65                                 + " ORDER BY p.PictureId ";
  66                 return result;
  67         }
  68
  69         /* (non-Javadoc)
  70          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  71          */
  72         @Override
  73         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  74                         String strQuery =
  75
  76                                 " SELECT p.*, f.*, pt.RIdentifier, p.PicturePhrase as FigurePhrase, p.PictureFile as fileName, p.PicturePath as filePath " +
  77                     " 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 "
  78                     +   " WHERE f.FactCategoryFk = 205 AND ( p.PictureID IN (" + ID_LIST_TOKEN + ")     )"
  79                     + " ORDER BY p.PictureId, f.factId, pt.RIdentifier ";
  80             ;
  81                 return strQuery;
  82         }
  83
  84         /* (non-Javadoc)
  85          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
  86          */
  87         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
  88                 boolean success = true;
  89
  90                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
  91
  92 //              Set<SpecimenOrObservationBase> specimenToSave = new HashSet<SpecimenOrObservationBase>();
  93                 Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
  94
  95 //              Map<String, DerivedUnitBase> ecoFactMap = (Map<String, DerivedUnitBase>) partitioner.getObjectMap(AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE);
  96                 Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
  97                 Map<String, DerivedUnitBase<?>> specimenMap = (Map<String, DerivedUnitBase<?>>) partitioner.getObjectMap(AlgaTerraFactEcologyImport.FACT_ECOLOGY_NAMESPACE);
  98
  99                 ResultSet rs = partitioner.getResultSet();
 100
 101                 try {
 102
 103                         int i = 0;
 104
 105                         //for each reference
 106             while (rs.next()){
 107
 108                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 109
 110                                 int pictureId = rs.getInt("PictureID");
 111                                 int taxonId = rs.getInt("RIdentifier");
 112                                 int factId = rs.getInt("FactId");
 113
 114
 115                                 //TODO etc. Created, Notes, Copyright, TermsOfUse etc.
 116
 117                                 try {
 118
 119                                         TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));
 120                                         if (taxonBase == null){
 121                                                 logger.warn("Could not find taxon (" + taxonId +") for picture fact " +  factId);
 122                                         }else if (! taxonBase.isInstanceOf(Taxon.class)){
 123                                                 logger.warn("Taxon is not of class Taxon but " + taxonBase.getClass() + ". RIdentifier: " + taxonId + " PictureId: " +  pictureId + ", FactId: "+  factId);
 124
 125                                         }else{
 126                                                 Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 127
 128                                                 Media media = handleSingleImage(rs, taxon, state, partitioner);
 129
 130                                                 handlePictureSpecificFields(rs, media, state, specimenMap);
 131
 132                                                 taxaToSave.add(taxon);
 133                                         }
 134
 135
 136                                 } catch (Exception e) {
 137                                         logger.warn("Exception in " + getTableName() + ": PictureId " + pictureId + ". " + e.getMessage());
 138                                         e.printStackTrace();
 139                                 }
 140
 141             }
 142
 143 //            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
 144
 145                         logger.warn(pluralString + " to save: " + taxaToSave.size());
 146 //                      getOccurrenceService().save(taxaToSave);
 147                         getTaxonService().save(taxaToSave);
 148
 149                         return success;
 150                 } catch (SQLException e) {
 151                         logger.error("SQLException:" +  e);
 152                         return false;
 153                 }
 154         }
 155
 156
 157
 158         private void handlePictureSpecificFields(ResultSet rs, Media media, AlgaTerraImportState state, Map<String, DerivedUnitBase<?>> specimenMap) throws SQLException {
 159                 Integer specimenFactId = nullSafeInt(rs, "FactFk");
 160                 if (specimenFactId != null){
 161                         DerivedUnitBase<?> specimen = specimenMap.get(String.valueOf(specimenFactId));
 162                         if (specimen == null){
 163                                 logger.warn("Specimen not found for FactFK: " + specimenFactId);
 164                         }else{
 165                                 try {
 166                                         DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(specimen);
 167                                         facade.addDerivedUnitMedia(media);
 168                                         getOccurrenceService().saveOrUpdate(specimen);
 169                                 } catch (DerivedUnitFacadeNotSupportedException e) {
 170                                         e.printStackTrace();
 171                                         logger.error(e.getMessage());
 172                                 }
 173                         }
 174                 }
 175
 176         }
 177
 178
 179         /* (non-Javadoc)
 180          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 181          */
 182         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 183                 String nameSpace;
 184                 Class cdmClass;
 185                 Set<String> idSet;
 186                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 187
 188                 try{
 189                         Set<String> taxonIdSet = new HashSet<String>();
 190                         Set<String> specimenIdSet = new HashSet<String>();
 191
 192                         while (rs.next()){
 193                                 handleForeignKey(rs, taxonIdSet, "RIdentifier");
 194                                 handleForeignKey(rs, specimenIdSet, "FactFk");
 195                         }
 196
 197                         //taxon map
 198                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 199                         cdmClass = TaxonBase.class;
 200                         idSet = taxonIdSet;
 201                         Map<String, TaxonBase> taxonMap = (Map<String,TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 202                         result.put(nameSpace, taxonMap);
 203
 204                         //fact specimen map
 205                         nameSpace = AlgaTerraFactEcologyImport.FACT_ECOLOGY_NAMESPACE;
 206                         cdmClass = SpecimenOrObservationBase.class;
 207                         idSet = specimenIdSet;
 208                         Map<String, SpecimenOrObservationBase> specimenMap = (Map<String,SpecimenOrObservationBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 209                         result.put(nameSpace, specimenMap);
 210
 211
 212                 } catch (SQLException e) {
 213                         throw new RuntimeException(e);
 214                 }
 215                 return result;
 216         }
 217
 218
 219
 220
 221         /* (non-Javadoc)
 222          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 223          */
 224         @Override
 225         protected boolean doCheck(BerlinModelImportState state){
 226                 IOValidator<BerlinModelImportState> validator = new AlgaTerraTypeImportValidator();
 227                 return validator.validate(state);
 228         }
 229
 230         /* (non-Javadoc)
 231          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 232          */
 233         protected boolean isIgnore(BerlinModelImportState bmState){
 234                 AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator();
 235                 return !  ( config.isDoTypes() && config.isDoImages()) ;
 236         }
 237
 238 }