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.commons.lang.StringUtils;
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  24 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;
  25 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  26 import eu.etaxonomy.cdm.database.update.TableNameChanger;
  27 import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraTypeImportValidator;
  28 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  29 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  30 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelReferenceImport;
  31 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameImport;
  32 import eu.etaxonomy.cdm.io.common.IOValidator;
  33 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  34 import eu.etaxonomy.cdm.model.common.CdmBase;
  35 import eu.etaxonomy.cdm.model.media.Media;
  36 import eu.etaxonomy.cdm.model.name.BotanicalName;
  37 import eu.etaxonomy.cdm.model.name.Rank;
  38 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  39 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  40 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  41 import eu.etaxonomy.cdm.model.occurrence.Collection;
  42 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  43 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  44 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  45 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47
  48
  49 /**
  50  * @author a.mueller
  51  * @created 20.03.2008
  52  * @version 1.0
  53  */
  54 @Component
  55 public class AlgaTerraTypeImagesImport  extends AlgaTerraImageImportBase {
  56         private static final Logger logger = Logger.getLogger(AlgaTerraTypeImagesImport.class);
  57
  58
  59         private static int modCount = 5000;
  60         private static final String pluralString = "type images";
  61         private static final String dbTableName = "SpecimenFigure";  //??
  62
  63         public AlgaTerraTypeImagesImport(){
  64                 super();
  65         }
  66
  67
  68         /* (non-Javadoc)
  69          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  70          */
  71         @Override
  72         protected String getIdQuery(BerlinModelImportState state) {
  73                 String result = " SELECT SpecimenFigureId "
  74                                 + " FROM SpecimenFigure "
  75                                 + " WHERE TypeSpecimenFk is NOT NULL "
  76                                 + " ORDER BY TypeSpecimenFk ";
  77                 return result;
  78         }
  79
  80         /* (non-Javadoc)
  81          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  82          */
  83         @Override
  84         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  85                         String strQuery =
  86
  87                         " SELECT sf.*, sf.SpecimenFigurePhrase as FigurePhrase, sf.SpecimenFigure as fileName" +
  88             " FROM SpecimenFigure sf  "
  89         +       " WHERE (sf.SpecimenFigureId IN (" + ID_LIST_TOKEN + ")  )"
  90         + " ORDER BY TypeSpecimenFk ";
  91             ;
  92                 return strQuery;
  93         }
  94
  95         /* (non-Javadoc)
  96          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
  97          */
  98         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
  99                 boolean success = true;
 100
 101                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
 102
 103                 Set<SpecimenOrObservationBase> unitsToSave = new HashSet<SpecimenOrObservationBase>();
 104
 105                 Map<String, DerivedUnit> typeSpecimenMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(AlgaTerraSpecimenImportBase.TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE);
 106                 Map<String, Reference> biblioReference = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
 107
 108
 109                 ResultSet rs = partitioner.getResultSet();
 110
 111                 try {
 112
 113                         int i = 0;
 114
 115                         //for each reference
 116             while (rs.next()){
 117
 118                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 119
 120                                 int figureId = rs.getInt("SpecimenFigureId");
 121                                 int typeSpecimenFk = rs.getInt("typeSpecimenFk");
 122
 123
 124                                 //TODO etc. Created, Notes, Copyright, TermsOfUse etc.
 125
 126                                 try {
 127
 128                                         //source ref
 129                                         Reference<?> sourceRef = state.getTransactionalSourceReference();
 130
 131                                         DerivedUnitBase derivedUnit = typeSpecimenMap.get(String.valueOf(typeSpecimenFk));
 132
 133                                         if (derivedUnit == null){
 134                                                 logger.warn("Could not find type specimen (" + typeSpecimenFk +") for specimen figure " +  figureId);
 135                                         }else{
 136
 137                                                 //field observation
 138                                                 Media media = handleSingleImage(rs, derivedUnit, state, partitioner);
 139
 140                                                 handleTypeImageSpecificFields(rs, media, state);
 141
 142                                                 unitsToSave.add(derivedUnit);
 143                                         }
 144
 145
 146                                 } catch (Exception e) {
 147                                         logger.warn("Exception in " + getTableName() + ": SpecimenFigureId " + figureId + ". " + e.getMessage());
 148                                         e.printStackTrace();
 149                                 }
 150
 151             }
 152
 153 //            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
 154
 155                         logger.warn(pluralString + " to save: " + unitsToSave.size());
 156                         getOccurrenceService().saveOrUpdate(unitsToSave);
 157
 158                         return success;
 159                 } catch (SQLException e) {
 160                         logger.error("SQLException:" +  e);
 161                         return false;
 162                 }
 163         }
 164
 165
 166
 167         private void handleTypeImageSpecificFields(ResultSet rs, Media media, AlgaTerraImportState state) throws SQLException {
 168                 //TODO
 169
 170         }
 171
 172
 173         /* (non-Javadoc)
 174          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 175          */
 176         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 177                 String nameSpace;
 178                 Class cdmClass;
 179                 Set<String> idSet;
 180                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 181
 182                 try{
 183                         Set<String> typeSpecimenIdSet = new HashSet<String>();
 184
 185                         while (rs.next()){
 186                                 handleForeignKey(rs, typeSpecimenIdSet, "TypeSpecimenFk");
 187                         }
 188
 189                         //type specimen map
 190                         nameSpace = AlgaTerraSpecimenImportBase.TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE;
 191                         cdmClass = SpecimenOrObservationBase.class;
 192                         idSet = typeSpecimenIdSet;
 193                         Map<String, DerivedUnit> typeSpecimenMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 194                         result.put(nameSpace, typeSpecimenMap);
 195
 196
 197                 } catch (SQLException e) {
 198                         throw new RuntimeException(e);
 199                 }
 200                 return result;
 201         }
 202
 203
 204
 205
 206         /* (non-Javadoc)
 207          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 208          */
 209         @Override
 210         protected boolean doCheck(BerlinModelImportState state){
 211                 IOValidator<BerlinModelImportState> validator = new AlgaTerraTypeImportValidator();
 212                 return validator.validate(state);
 213         }
 214
 215         /* (non-Javadoc)
 216          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
 217          */
 218         @Override
 219         protected String getTableName() {
 220                 return dbTableName;
 221         }
 222
 223         /* (non-Javadoc)
 224          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
 225          */
 226         @Override
 227         public String getPluralString() {
 228                 return pluralString;
 229         }
 230
 231         /* (non-Javadoc)
 232          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 233          */
 234         protected boolean isIgnore(BerlinModelImportState bmState){
 235                 AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator();
 236 //              return !  ( config.isDoTypes() && config.isDoImages()) ;
 237                 return false;
 238         }
 239
 240 }