app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImagesImport.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.BerlinModelReferenceImport;
  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.occurrence.DerivedUnit;
  31 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  32 import eu.etaxonomy.cdm.model.reference.Reference;
  33
  34
  35 /**
  36  * @author a.mueller
  37  * @created 20.03.2008
  38  */
  39 @Component
  40 public class AlgaTerraTypeImagesImport  extends AlgaTerraImageImportBase {
  41         private static final Logger logger = Logger.getLogger(AlgaTerraTypeImagesImport.class);
  42
  43
  44         private static int modCount = 5000;
  45         private static final String pluralString = "type images";
  46         private static final String dbTableName = "SpecimenFigure";  //??
  47
  48         public AlgaTerraTypeImagesImport(){
  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 SpecimenFigureId "
  59                                 + " FROM SpecimenFigure "
  60                                 + " WHERE TypeSpecimenFk is NOT NULL "
  61                                 + " ORDER BY TypeSpecimenFk ";
  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 sf.*, sf.SpecimenFigurePhrase as FigurePhrase, sf.SpecimenFigure as fileName, sf.PicturePath as filePath" +
  73             " FROM SpecimenFigure sf  "
  74         +       " WHERE (sf.SpecimenFigureId IN (" + ID_LIST_TOKEN + ")  )"
  75         + " ORDER BY TypeSpecimenFk ";
  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         @Override
  84     public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
  85                 boolean success = true;
  86
  87                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
  88
  89                 Set<SpecimenOrObservationBase> unitsToSave = new HashSet<SpecimenOrObservationBase>();
  90
  91                 Map<String, DerivedUnit> typeSpecimenMap = partitioner.getObjectMap(AlgaTerraSpecimenImportBase.TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE);
  92                 Map<String, Reference> referenceMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
  93
  94
  95                 ResultSet rs = partitioner.getResultSet();
  96
  97                 try {
  98
  99                         int i = 0;
 100
 101                         //for each reference
 102             while (rs.next()){
 103
 104                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 105
 106                                 int figureId = rs.getInt("SpecimenFigureId");
 107                                 int typeSpecimenFk = rs.getInt("typeSpecimenFk");
 108
 109
 110                                 //TODO etc. Created, Notes, Copyright, TermsOfUse etc.
 111
 112                                 try {
 113
 114                                         //source ref
 115                                         Reference sourceRef = state.getTransactionalSourceReference();
 116
 117                                         DerivedUnit derivedUnit = typeSpecimenMap.get(String.valueOf(typeSpecimenFk));
 118
 119                                         if (derivedUnit == null){
 120                                                 logger.warn("Could not find type specimen (" + typeSpecimenFk +") for specimen figure " +  figureId);
 121                                         }else{
 122
 123                                                 //field observation
 124                                                 Media media = handleSingleImage(rs, derivedUnit, state, partitioner, PathType.Image);
 125
 126                                                 handleTypeImageSpecificFields(rs, media, state);
 127
 128                                                 unitsToSave.add(derivedUnit);
 129                                         }
 130
 131
 132                                 } catch (Exception e) {
 133                                         logger.warn("Exception in " + getTableName() + ": SpecimenFigureId " + figureId + ". " + e.getMessage());
 134                                         e.printStackTrace();
 135                                 }
 136
 137             }
 138
 139 //            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
 140
 141                         logger.warn(pluralString + " to save: " + unitsToSave.size());
 142                         getOccurrenceService().saveOrUpdate(unitsToSave);
 143
 144                         return success;
 145                 } catch (SQLException e) {
 146                         logger.error("SQLException:" +  e);
 147                         return false;
 148                 }
 149         }
 150
 151
 152
 153         private void handleTypeImageSpecificFields(ResultSet rs, Media media, AlgaTerraImportState state) throws SQLException {
 154                 //TODO refFk, refDetailFk, publishFlag
 155                 Integer refFk = nullSafeInt(rs, "refFk");
 156                 Integer refDetailFk = nullSafeInt(rs, "refDetailFk");
 157
 158                 //TODO
 159
 160
 161         }
 162
 163         @Override
 164         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
 165                 String nameSpace;
 166                 Class<?> cdmClass;
 167                 Set<String> idSet;
 168                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 169
 170                 try{
 171                         Set<String> typeSpecimenIdSet = new HashSet<String>();
 172
 173                         while (rs.next()){
 174                                 handleForeignKey(rs, typeSpecimenIdSet, "TypeSpecimenFk");
 175                         }
 176
 177                         //type specimen map
 178                         nameSpace = AlgaTerraSpecimenImportBase.TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE;
 179                         cdmClass = SpecimenOrObservationBase.class;
 180                         idSet = typeSpecimenIdSet;
 181                         Map<String, DerivedUnit> typeSpecimenMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 182                         result.put(nameSpace, typeSpecimenMap);
 183
 184
 185                 } catch (SQLException e) {
 186                         throw new RuntimeException(e);
 187                 }
 188                 return result;
 189         }
 190
 191         @Override
 192         protected boolean doCheck(BerlinModelImportState state){
 193                 IOValidator<BerlinModelImportState> validator = new AlgaTerraTypeImportValidator();
 194                 return validator.validate(state);
 195         }
 196
 197
 198         @Override
 199         protected boolean isIgnore(BerlinModelImportState bmState){
 200                 AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator();
 201                 return !  ( config.isDoTypes() && config.isDoImages()) ;
 202 //              return false;
 203         }
 204
 205 }