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.occurrence.Collection;
  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 01.09.2012
  38  */
  39 @Component
  40 public class AlgaTerraCollectionImport  extends BerlinModelImportBase {
  41         private static final Logger logger = Logger.getLogger(AlgaTerraCollectionImport.class);
  42
  43
  44         private static int modCount = 5000;
  45         private static final String pluralString = "collections";
  46         private static final String dbTableName = "Collection";  //??
  47
  48         public static final String NAMESPACE_COLLECTION = "Collection";
  49         public static final String NAMESPACE_SUBCOLLECTION = "Collection (Subcollection)";
  50
  51
  52         public AlgaTerraCollectionImport(){
  53                 super();
  54         }
  55
  56
  57
  58         /* (non-Javadoc)
  59          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  60          */
  61         @Override
  62         protected String getIdQuery(BerlinModelImportState state) {
  63                 String result = " SELECT CollectionId " +
  64                                 " FROM Collection c "
  65                                 + " ORDER BY partOfFk, c.CollectionId ";
  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             " SELECT CollectionId, Name, Town, IHCode, Subcollection, partOfFk, TDWGGazetteerFk, Address, CultCollFlag, " +
  76                         " Created_When, Updated_When, Created_Who, Updated_Who, Notes " +
  77             " FROM Collection c " +
  78             " WHERE c.CollectionId IN (" + ID_LIST_TOKEN + ") "
  79             + " ORDER BY partOfFk, c.CollectionId "
  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                 Set<Collection> collectionsToSave = new HashSet<Collection>();
  92
  93
  94                 Map<String, Collection> collectionMap = (Map<String, Collection>) partitioner.getObjectMap(NAMESPACE_COLLECTION);
  95
  96
  97                 ResultSet rs = partitioner.getResultSet();
  98
  99                 try {
 100
 101                         int i = 0;
 102
 103                         //for each reference
 104             while (rs.next()){
 105
 106                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
 107
 108                         int collectionId = rs.getInt("CollectionId");
 109                         String name = rs.getString("Name");
 110                         String town = rs.getString("Town");
 111                         String ihCode = rs.getString("IHCode");
 112                         String subCollectionStr = rs.getString("Subcollection");
 113                         Integer partOfFk = nullSafeInt(rs, "PartOfFk");
 114
 115 //                      Integer tdwgArea = nullSafeInt(rs, "TDWGGazetteerFk");  //somehow redundant with town
 116 //                      String address = rs.getString("Address");           //only available for BGBM
 117 //                      Boolean cultCollFlag = rs.getBoolean("CultCollFlag");  //?? not really needed according to Henning
 118
 119                         //TODO createdUpdates, NOtes
 120
 121                         try {
 122
 123                                         //source ref
 124                                         Reference<?> sourceRef = state.getTransactionalSourceReference();
 125
 126
 127                                         //collection
 128                                         Collection collection;
 129                                         if (partOfFk == null){
 130                                                 collection = makeCollection(collectionsToSave,
 131                                                                 collectionId, name, town, ihCode, sourceRef, NAMESPACE_COLLECTION, collectionMap);
 132                                         }else{
 133                                                 collection = collectionMap.get(String.valueOf(partOfFk));
 134                                                 if (collection == null){
 135                                                         logger.warn("PartOf collection not found");
 136                                                 }
 137                                         }
 138
 139
 140                                         //subcollection
 141                                         if (isNotBlank(subCollectionStr)){
 142                                                 Collection subCollection = makeCollection(collectionsToSave, collectionId, subCollectionStr, town, ihCode, sourceRef, NAMESPACE_SUBCOLLECTION, collectionMap);
 143                                                 subCollection.setSuperCollection(collection);
 144                                         }
 145
 146
 147                                         //TODO movedToFk (extension ??)
 148
 149
 150                                 } catch (Exception e) {
 151                                         logger.warn("Exception in collection: CollectionId " + collectionId + ". " + e.getMessage());
 152 //                                      e.printStackTrace();
 153                                 }
 154
 155             }
 156
 157                         logger.warn(pluralString + " to save: " + collectionsToSave.size());
 158                         getCollectionService().save(collectionsToSave);
 159
 160                         return success;
 161                 } catch (SQLException e) {
 162                         logger.error("SQLException:" +  e);
 163                         return false;
 164                 }
 165         }
 166
 167
 168
 169         /**
 170          * @param collectionsToSave
 171          * @param collectionId
 172          * @param name
 173          * @param town
 174          * @param ihCode
 175          * @param sourceRef
 176          * @param collectionMap
 177          * @return
 178          */
 179         private Collection makeCollection(Set<Collection> collectionsToSave, int collectionId,
 180                         String name, String town, String ihCode, Reference<?> sourceRef, String namespace, Map<String, Collection> collectionMap) {
 181                 Collection collection = Collection.NewInstance();
 182                 collection.setName(name);
 183                 if (isNotBlank(ihCode)){
 184                         collection.setCode(ihCode);
 185                         collection.setCodeStandard("Index Herbariorum");
 186                 }
 187
 188                 collection.setTownOrLocation(town);
 189                 collection.addSource(String.valueOf(collectionId), namespace, sourceRef, null);
 190
 191                 collectionMap.put(String.valueOf(collectionId), collection);
 192                 collectionsToSave.add(collection);  //or subcollection ?
 193                 return collection;
 194         }
 195
 196
 197
 198         /* (non-Javadoc)
 199          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 200          */
 201         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 202                 String nameSpace;
 203                 Class cdmClass;
 204                 Set<String> idSet;
 205                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 206
 207                 try{
 208                         Set<String> collectionIdSet = new HashSet<String>();
 209
 210                         while (rs.next()){
 211                                 handleForeignKey(rs, collectionIdSet, "partOfFk");
 212                         }
 213
 214                         //type specimen map
 215                         nameSpace = NAMESPACE_COLLECTION;
 216                         cdmClass = Collection.class;
 217                         idSet = collectionIdSet;
 218                         Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 219                         result.put(nameSpace, collectionMap);
 220
 221
 222                 } catch (SQLException e) {
 223                         throw new RuntimeException(e);
 224                 }
 225                 return result;
 226
 227         }
 228
 229
 230         /* (non-Javadoc)
 231          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 232          */
 233         @Override
 234         protected boolean doCheck(BerlinModelImportState state){
 235                 IOValidator<BerlinModelImportState> validator = new AlgaTerraCollectionImportValidator();
 236                 return validator.validate(state);
 237         }
 238
 239         /* (non-Javadoc)
 240          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
 241          */
 242         @Override
 243         protected String getTableName() {
 244                 return dbTableName;
 245         }
 246
 247         /* (non-Javadoc)
 248          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
 249          */
 250         @Override
 251         public String getPluralString() {
 252                 return pluralString;
 253         }
 254
 255         /* (non-Javadoc)
 256          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 257          */
 258         protected boolean isIgnore(BerlinModelImportState bmState){
 259                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
 260                 return ! ( state.getAlgaTerraConfigurator().isDoEcoFacts() ||  state.getAlgaTerraConfigurator().isDoTypes() );
 261         }
 262
 263 }