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.DbImportDescriptionElementSourceCreationMapper;
  26 import eu.etaxonomy.cdm.io.common.mapping.DbImportDistributionCreationMapper;
  27 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  28 import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectMapper;
  29 import eu.etaxonomy.cdm.io.common.mapping.DbNotYetImplementedMapper;
  30 import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsReferenceImportValidator;
  31 import eu.etaxonomy.cdm.model.common.AnnotationType;
  32 import eu.etaxonomy.cdm.model.common.CdmBase;
  33 import eu.etaxonomy.cdm.model.description.Distribution;
  34 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  35 import eu.etaxonomy.cdm.model.location.NamedArea;
  36 import eu.etaxonomy.cdm.model.reference.Reference;
  37 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  38
  39
  40 /**
  41  * @author a.mueller
  42  * @created 20.02.2010
  43  * @version 1.0
  44  */
  45 @Component
  46 public class ErmsDrImport  extends ErmsImportBase<Distribution> {
  47         @SuppressWarnings("unused")
  48         private static final Logger logger = Logger.getLogger(ErmsDrImport.class);
  49
  50         private DbImportMapping mapping;
  51
  52         private int modCount = 10000;
  53         private static final String pluralString = "distributions";
  54         private static final String dbTableName = "dr";
  55         private static final Class cdmTargetClass = Distribution.class;
  56
  57         public ErmsDrImport(){
  58                 super(pluralString, dbTableName, cdmTargetClass);
  59         }
  60
  61
  62         /* (non-Javadoc)
  63          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  64          */
  65         @Override
  66         protected String getRecordQuery(ErmsImportConfigurator config) {
  67                 String strRecordQuery =
  68                         " SELECT dr.*, tu.tu_acctaxon, tu.id " +
  69                         " FROM dr INNER JOIN tu ON dr.tu_id = tu.id " +
  70                         " WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";
  71                 return strRecordQuery;
  72         }
  73
  74         /* (non-Javadoc)
  75          * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
  76          */
  77         protected DbImportMapping getMapping() {
  78                 if (mapping == null){
  79                         mapping = new DbImportMapping();
  80
  81                         PresenceTerm status = PresenceTerm.PRESENT();
  82                         DbImportDistributionCreationMapper<?> distributionMapper = DbImportDistributionCreationMapper.NewFixedStatusInstance("id", DR_NAMESPACE, "tu_acctaxon", ErmsTaxonImport.TAXON_NAMESPACE, status);
  83                         distributionMapper.setSource("source_id", REFERENCE_NAMESPACE, null);
  84                         mapping.addMapper(distributionMapper);
  85
  86                         mapping.addMapper(DbImportObjectMapper.NewInstance("gu_id", "area", ErmsAreaImport.AREA_NAMESPACE));
  87                         mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL()));
  88
  89                         mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptsource_id"));
  90                         mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptreason"));
  91                         mapping.addMapper(DbIgnoreMapper.NewInstance("valid_flag"));
  92                         mapping.addMapper(DbIgnoreMapper.NewInstance("certain_flag"));
  93                         mapping.addMapper(DbIgnoreMapper.NewInstance("map_flag"));
  94                         mapping.addMapper(DbIgnoreMapper.NewInstance("endemic_flag"));
  95                         mapping.addMapper(DbIgnoreMapper.NewInstance("exotic_flag"));
  96                         mapping.addMapper(DbIgnoreMapper.NewInstance("typelocality_flag"));
  97                         mapping.addMapper(DbIgnoreMapper.NewInstance("specimenflag"));
  98                         mapping.addMapper(DbIgnoreMapper.NewInstance("lat"));
  99                         mapping.addMapper(DbIgnoreMapper.NewInstance("long"));
 100                         mapping.addMapper(DbIgnoreMapper.NewInstance("depthshallow"));
 101                         mapping.addMapper(DbIgnoreMapper.NewInstance("depthdeep"));
 102                         mapping.addMapper(DbIgnoreMapper.NewInstance("beginyear"));
 103                         mapping.addMapper(DbIgnoreMapper.NewInstance("beginmonth"));
 104                         mapping.addMapper(DbIgnoreMapper.NewInstance("beginday"));
 105                         mapping.addMapper(DbIgnoreMapper.NewInstance("endyear"));
 106                         mapping.addMapper(DbIgnoreMapper.NewInstance("endmonth"));
 107                         mapping.addMapper(DbIgnoreMapper.NewInstance("endday"));
 108                         mapping.addMapper(DbIgnoreMapper.NewInstance("min_abundance"));
 109                         mapping.addMapper(DbIgnoreMapper.NewInstance("max_abundance"));
 110
 111
 112                 }
 113                 return mapping;
 114         }
 115
 116         /* (non-Javadoc)
 117          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 118          */
 119         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 120                 String nameSpace;
 121                 Class cdmClass;
 122                 Set<String> idSet;
 123                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 124
 125                 try{
 126                         Set<String> taxonIdSet = new HashSet<String>();
 127                         Set<String> areaIdSet = new HashSet<String>();
 128                         Set<String> sourceIdSet = new HashSet<String>();
 129                         while (rs.next()){
 130                                 handleForeignKey(rs, taxonIdSet,"tu_acctaxon" );
 131                                 handleForeignKey(rs, areaIdSet, "gu_id");
 132                                 handleForeignKey(rs, sourceIdSet, "source_id");
 133                         }
 134
 135                         //taxon map
 136                         nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
 137                         cdmClass = TaxonBase.class;
 138                         idSet = taxonIdSet;
 139                         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 140                         result.put(nameSpace, taxonMap);
 141
 142                         //areas
 143                         nameSpace = ErmsAreaImport.AREA_NAMESPACE;
 144                         cdmClass = NamedArea.class;
 145                         idSet = areaIdSet;
 146                         Map<String, NamedArea> areaMap = (Map<String, NamedArea>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 147                         result.put(nameSpace, areaMap);
 148
 149                         //reference map
 150                         nameSpace = ErmsReferenceImport.REFERENCE_NAMESPACE;
 151                         cdmClass = Reference.class;
 152                         idSet = sourceIdSet;
 153                         Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 154                         result.put(nameSpace, referenceMap);
 155
 156
 157                 } catch (SQLException e) {
 158                         throw new RuntimeException(e);
 159                 }
 160                 return result;
 161         }
 162
 163         /**
 164          * @param distribution
 165          * @param source_id
 166          * @param state
 167          */
 168         private void addSource(Distribution distribution, Integer source_id, ErmsImportState state) {
 169                 Reference ref = (Reference)state.getRelatedObject(ErmsReferenceImport.REFERENCE_NAMESPACE, String.valueOf(source_id));
 170                 distribution.addSource(null, null, ref, null);
 171         }
 172
 173         /* (non-Javadoc)
 174          * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
 175          */
 176         public Distribution createObject(ResultSet rs, ErmsImportState state)
 177                         throws SQLException {
 178                 return null;  //not needed
 179         }
 180
 181
 182         /* (non-Javadoc)
 183          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 184          */
 185         @Override
 186         protected boolean doCheck(ErmsImportState state){
 187                 IOValidator<ErmsImportState> validator = new ErmsReferenceImportValidator();
 188                 return validator.validate(state);
 189         }
 190
 191         /* (non-Javadoc)
 192          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 193          */
 194         protected boolean isIgnore(ErmsImportState state){
 195                 return ! state.getConfig().isDoOccurrence();
 196         }
 197
 198
 199
 200
 201 }