cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsDrImport.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.pesi.erms;
  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.common.IOValidator;
  23 import eu.etaxonomy.cdm.io.common.mapping.DbIgnoreMapper;
  24 import eu.etaxonomy.cdm.io.common.mapping.DbImportAnnotationMapper;
  25 import eu.etaxonomy.cdm.io.common.mapping.DbImportDistributionCreationMapper;
  26 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  27 import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectMapper;
  28 import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsDrImportValidator;
  29 import eu.etaxonomy.cdm.model.common.AnnotationType;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.description.Distribution;
  32 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  33 import eu.etaxonomy.cdm.model.location.NamedArea;
  34 import eu.etaxonomy.cdm.model.reference.Reference;
  35 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  36
  37
  38 /**
  39  * @author a.mueller
  40  * @created 20.02.2010
  41  * @version 1.0
  42  */
  43 @Component
  44 public class ErmsDrImport  extends ErmsImportBase<Distribution> {
  45         @SuppressWarnings("unused")
  46         private static final Logger logger = Logger.getLogger(ErmsDrImport.class);
  47
  48         private DbImportMapping mapping;
  49
  50         private int modCount = 10000;
  51         private static final String pluralString = "distributions";
  52         private static final String dbTableName = "dr";
  53         private static final Class cdmTargetClass = Distribution.class;
  54
  55         public ErmsDrImport(){
  56                 super(pluralString, dbTableName, cdmTargetClass);
  57         }
  58
  59
  60         /* (non-Javadoc)
  61          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  62          */
  63         @Override
  64         protected String getRecordQuery(ErmsImportConfigurator config) {
  65                 String strRecordQuery =
  66                         " SELECT dr.*, tu.tu_acctaxon, tu.id " +
  67                         " FROM dr INNER JOIN tu ON dr.tu_id = tu.id " +
  68                         " WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";
  69                 return strRecordQuery;
  70         }
  71
  72         /* (non-Javadoc)
  73          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
  74          */
  75         protected DbImportMapping getMapping() {
  76                 if (mapping == null){
  77                         mapping = new DbImportMapping();
  78
  79                         PresenceTerm status = PresenceTerm.PRESENT();
  80                         DbImportDistributionCreationMapper<?> distributionMapper = DbImportDistributionCreationMapper.NewFixedStatusInstance("id", DR_NAMESPACE, "tu_acctaxon", ErmsTaxonImport.TAXON_NAMESPACE, status);
  81                         distributionMapper.setSource("source_id", REFERENCE_NAMESPACE, null);
  82                         mapping.addMapper(distributionMapper);
  83
  84                         mapping.addMapper(DbImportObjectMapper.NewInstance("gu_id", "area", ErmsAreaImport.AREA_NAMESPACE));
  85                         mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL()));
  86
  87                         mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptsource_id"));
  88                         mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptreason"));
  89                         mapping.addMapper(DbIgnoreMapper.NewInstance("valid_flag"));
  90                         mapping.addMapper(DbIgnoreMapper.NewInstance("certain_flag"));
  91                         mapping.addMapper(DbIgnoreMapper.NewInstance("map_flag"));
  92                         mapping.addMapper(DbIgnoreMapper.NewInstance("endemic_flag"));
  93                         mapping.addMapper(DbIgnoreMapper.NewInstance("exotic_flag"));
  94                         mapping.addMapper(DbIgnoreMapper.NewInstance("typelocality_flag"));
  95                         mapping.addMapper(DbIgnoreMapper.NewInstance("specimenflag"));
  96                         mapping.addMapper(DbIgnoreMapper.NewInstance("lat"));
  97                         mapping.addMapper(DbIgnoreMapper.NewInstance("long"));
  98                         mapping.addMapper(DbIgnoreMapper.NewInstance("depthshallow"));
  99                         mapping.addMapper(DbIgnoreMapper.NewInstance("depthdeep"));
 100                         mapping.addMapper(DbIgnoreMapper.NewInstance("beginyear"));
 101                         mapping.addMapper(DbIgnoreMapper.NewInstance("beginmonth"));
 102                         mapping.addMapper(DbIgnoreMapper.NewInstance("beginday"));
 103                         mapping.addMapper(DbIgnoreMapper.NewInstance("endyear"));
 104                         mapping.addMapper(DbIgnoreMapper.NewInstance("endmonth"));
 105                         mapping.addMapper(DbIgnoreMapper.NewInstance("endday"));
 106                         mapping.addMapper(DbIgnoreMapper.NewInstance("min_abundance"));
 107                         mapping.addMapper(DbIgnoreMapper.NewInstance("max_abundance"));
 108
 109
 110                 }
 111                 return mapping;
 112         }
 113
 114         /* (non-Javadoc)
 115          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 116          */
 117         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 118                 String nameSpace;
 119                 Class cdmClass;
 120                 Set<String> idSet;
 121                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 122
 123                 try{
 124                         Set<String> taxonIdSet = new HashSet<String>();
 125                         Set<String> areaIdSet = new HashSet<String>();
 126                         Set<String> sourceIdSet = new HashSet<String>();
 127                         while (rs.next()){
 128                                 handleForeignKey(rs, taxonIdSet,"tu_acctaxon" );
 129                                 handleForeignKey(rs, areaIdSet, "gu_id");
 130                                 handleForeignKey(rs, sourceIdSet, "source_id");
 131                         }
 132
 133                         //taxon map
 134                         nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
 135                         cdmClass = TaxonBase.class;
 136                         idSet = taxonIdSet;
 137                         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 138                         result.put(nameSpace, taxonMap);
 139
 140                         //areas
 141                         nameSpace = ErmsAreaImport.AREA_NAMESPACE;
 142                         cdmClass = NamedArea.class;
 143                         idSet = areaIdSet;
 144                         Map<String, NamedArea> areaMap = (Map<String, NamedArea>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 145                         result.put(nameSpace, areaMap);
 146
 147                         //reference map
 148                         nameSpace = ErmsReferenceImport.REFERENCE_NAMESPACE;
 149                         cdmClass = Reference.class;
 150                         idSet = sourceIdSet;
 151                         Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 152                         result.put(nameSpace, referenceMap);
 153
 154
 155                 } catch (SQLException e) {
 156                         throw new RuntimeException(e);
 157                 }
 158                 return result;
 159         }
 160
 161         /**
 162          * @param distribution
 163          * @param source_id
 164          * @param state
 165          */
 166         private void addSource(Distribution distribution, Integer source_id, ErmsImportState state) {
 167                 Reference ref = (Reference)state.getRelatedObject(ErmsReferenceImport.REFERENCE_NAMESPACE, String.valueOf(source_id));
 168                 distribution.addSource(null, null, ref, null);
 169         }
 170
 171         /* (non-Javadoc)
 172          * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
 173          */
 174         public Distribution createObject(ResultSet rs, ErmsImportState state)
 175                         throws SQLException {
 176                 return null;  //not needed
 177         }
 178
 179
 180         /* (non-Javadoc)
 181          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 182          */
 183         @Override
 184         protected boolean doCheck(ErmsImportState state){
 185                 IOValidator<ErmsImportState> validator = new ErmsDrImportValidator();
 186                 return validator.validate(state);
 187         }
 188
 189         /* (non-Javadoc)
 190          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 191          */
 192         protected boolean isIgnore(ErmsImportState state){
 193                 return ! state.getConfig().isDoOccurrence();
 194         }
 195
 196
 197
 198
 199 }