app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraCollectionImport.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.AlgaTerraCollectionImportValidator;
  23 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  25 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  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.common.OriginalSourceType;
  30 import eu.etaxonomy.cdm.model.occurrence.Collection;
  31 import eu.etaxonomy.cdm.model.reference.Reference;
  32
  33
  34 /**
  35  * @author a.mueller
  36  * @created 01.09.2012
  37  */
  38 @Component
  39 public class AlgaTerraCollectionImport  extends BerlinModelImportBase {
  40         private static final Logger logger = Logger.getLogger(AlgaTerraCollectionImport.class);
  41
  42
  43         private static int modCount = 5000;
  44         private static final String pluralString = "collections";
  45         private static final String dbTableName = "Collection";  //??
  46
  47         public static final String NAMESPACE_COLLECTION = "Collection";
  48         public static final String NAMESPACE_SUBCOLLECTION = "Collection (Subcollection)";
  49
  50
  51         public AlgaTerraCollectionImport(){
  52                 super(dbTableName, pluralString);
  53         }
  54
  55
  56         /* (non-Javadoc)
  57          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  58          */
  59         @Override
  60         protected String getIdQuery(BerlinModelImportState state) {
  61                 String result = " SELECT CollectionId " +
  62                                 " FROM Collection c "
  63                                 + " ORDER BY partOfFk, c.CollectionId ";
  64                 return result;
  65         }
  66
  67         /* (non-Javadoc)
  68          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  69          */
  70         @Override
  71         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  72                         String strQuery =
  73             " SELECT CollectionId, Name, Town, IHCode, Subcollection, partOfFk, TDWGGazetteerFk, Address, CultCollFlag, " +
  74                         " Created_When, Updated_When, Created_Who, Updated_Who, Notes " +
  75             " FROM Collection c " +
  76             " WHERE c.CollectionId IN (" + ID_LIST_TOKEN + ") "
  77             + " ORDER BY partOfFk, c.CollectionId "
  78             ;
  79                 return strQuery;
  80         }
  81
  82         /* (non-Javadoc)
  83          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
  84          */
  85         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
  86                 boolean success = true;
  87
  88                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
  89                 Set<Collection> collectionsToSave = new HashSet<Collection>();
  90
  91
  92                 Map<String, Collection> collectionMap = (Map<String, Collection>) partitioner.getObjectMap(NAMESPACE_COLLECTION);
  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 collectionId = rs.getInt("CollectionId");
 107                         String name = rs.getString("Name");
 108                         String town = rs.getString("Town");
 109                         String ihCode = rs.getString("IHCode");
 110                         String subCollectionStr = rs.getString("Subcollection");
 111                         Integer partOfFk = nullSafeInt(rs, "PartOfFk");
 112
 113 //                      Integer tdwgArea = nullSafeInt(rs, "TDWGGazetteerFk");  //somehow redundant with town
 114 //                      String address = rs.getString("Address");           //only available for BGBM
 115 //                      Boolean cultCollFlag = rs.getBoolean("CultCollFlag");  //?? not really needed according to Henning
 116
 117                         //TODO createdUpdates, NOtes
 118
 119                         try {
 120
 121                                         //source ref
 122                                         Reference<?> sourceRef = state.getTransactionalSourceReference();
 123
 124
 125                                         //collection
 126                                         Collection collection;
 127                                         if (partOfFk == null){
 128                                                 collection = makeCollection(collectionsToSave,
 129                                                                 collectionId, name, town, ihCode, sourceRef, NAMESPACE_COLLECTION, collectionMap);
 130                                         }else{
 131                                                 collection = collectionMap.get(String.valueOf(partOfFk));
 132                                                 if (collection == null){
 133                                                         logger.warn("PartOf collection not found");
 134                                                 }
 135                                         }
 136
 137
 138                                         //subcollection
 139                                         if (isNotBlank(subCollectionStr)){
 140                                                 Collection subCollection = makeCollection(collectionsToSave, collectionId, subCollectionStr, town, ihCode, sourceRef, NAMESPACE_SUBCOLLECTION, collectionMap);
 141                                                 subCollection.setSuperCollection(collection);
 142                                         }
 143
 144
 145                                         //TODO movedToFk (extension ??)
 146
 147
 148                                 } catch (Exception e) {
 149                                         logger.warn("Exception in collection: CollectionId " + collectionId + ". " + e.getMessage());
 150 //                                      e.printStackTrace();
 151                                 }
 152
 153             }
 154
 155                         logger.warn(pluralString + " to save: " + collectionsToSave.size());
 156                         getCollectionService().save(collectionsToSave);
 157
 158                         return success;
 159                 } catch (SQLException e) {
 160                         logger.error("SQLException:" +  e);
 161                         return false;
 162                 }
 163         }
 164
 165
 166
 167         /**
 168          * @param collectionsToSave
 169          * @param collectionId
 170          * @param name
 171          * @param town
 172          * @param ihCode
 173          * @param sourceRef
 174          * @param collectionMap
 175          * @return
 176          */
 177         private Collection makeCollection(Set<Collection> collectionsToSave, int collectionId,
 178                         String name, String town, String ihCode, Reference<?> sourceRef, String namespace, Map<String, Collection> collectionMap) {
 179                 Collection collection = Collection.NewInstance();
 180                 collection.setName(name);
 181                 if (isNotBlank(ihCode) && ! "--".equals(ihCode)){
 182                         collection.setCode(ihCode);
 183                         collection.setCodeStandard("Index Herbariorum");
 184                 }
 185
 186                 collection.setTownOrLocation(town);
 187                 collection.addSource(OriginalSourceType.Import, String.valueOf(collectionId), namespace, sourceRef, null);
 188
 189                 collectionMap.put(String.valueOf(collectionId), collection);
 190                 collectionsToSave.add(collection);  //or subcollection ?
 191                 return collection;
 192         }
 193
 194
 195
 196
 197         @Override
 198         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
 199                 String nameSpace;
 200                 Class cdmClass;
 201                 Set<String> idSet;
 202                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 203
 204                 try{
 205                         Set<String> collectionIdSet = new HashSet<String>();
 206
 207                         while (rs.next()){
 208                                 handleForeignKey(rs, collectionIdSet, "partOfFk");
 209                         }
 210
 211                         //type specimen map
 212                         nameSpace = NAMESPACE_COLLECTION;
 213                         cdmClass = Collection.class;
 214                         idSet = collectionIdSet;
 215                         Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 216                         result.put(nameSpace, collectionMap);
 217
 218
 219                 } catch (SQLException e) {
 220                         throw new RuntimeException(e);
 221                 }
 222                 return result;
 223
 224         }
 225
 226
 227         /* (non-Javadoc)
 228          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 229          */
 230         @Override
 231         protected boolean doCheck(BerlinModelImportState state){
 232                 IOValidator<BerlinModelImportState> validator = new AlgaTerraCollectionImportValidator();
 233                 return validator.validate(state);
 234         }
 235
 236         /* (non-Javadoc)
 237          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 238          */
 239         protected boolean isIgnore(BerlinModelImportState bmState){
 240                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
 241                 return ! ( state.getAlgaTerraConfigurator().isDoEcoFacts() ||  state.getAlgaTerraConfigurator().isDoTypes() );
 242         }
 243
 244 }