cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.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.indexFungorum;
  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.common.CdmUtils;
  24 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  25 import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
  26 import eu.etaxonomy.cdm.model.common.CdmBase;
  27 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  28 import eu.etaxonomy.cdm.model.name.NonViralName;
  29 import eu.etaxonomy.cdm.model.name.Rank;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.taxon.Classification;
  32 import eu.etaxonomy.cdm.model.taxon.Taxon;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  34 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  35
  36
  37 /**
  38  * @author a.mueller
  39  * @created 27.02.2012
  40  */
  41 @Component
  42 public class IndexFungorumSpeciesImport  extends IndexFungorumImportBase {
  43         private static final Logger logger = Logger.getLogger(IndexFungorumSpeciesImport.class);
  44
  45         private static final String pluralString = "species";
  46         private static final String dbTableName = "[tblPESIfungi-IFdata]";
  47
  48         public IndexFungorumSpeciesImport(){
  49                 super(pluralString, dbTableName, null);
  50         }
  51
  52
  53
  54
  55         @Override
  56         protected String getIdQuery() {
  57                 String result = " SELECT RECORD_NUMBER FROM " + getTableName() +
  58                                 " ORDER BY PreferredName ";
  59                 return result;
  60         }
  61
  62
  63
  64
  65         /* (non-Javadoc)
  66          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  67          */
  68         @Override
  69         protected String getRecordQuery(IndexFungorumImportConfigurator config) {
  70                 String strRecordQuery =
  71                                 " SELECT DISTINCT distribution.PreferredNameFDCnumber, species.* " +
  72                                 " FROM tblPESIfungi AS distribution RIGHT OUTER JOIN  dbo.[tblPESIfungi-IFdata] AS species ON distribution.PreferredNameIFnumber = species.RECORD_NUMBER " +
  73                         " WHERE ( species.RECORD_NUMBER IN (" + ID_LIST_TOKEN + ") )" +
  74                         "";
  75                 return strRecordQuery;
  76         }
  77
  78
  79         @Override
  80         public boolean doPartition(ResultSetPartitioner partitioner, IndexFungorumImportState state) {
  81                 boolean success = true;
  82                 Reference<?> sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
  83                 ResultSet rs = partitioner.getResultSet();
  84
  85                 Classification classification = getClassification(state);
  86                 try {
  87                         while (rs.next()){
  88
  89                                 //TODO
  90                                 //DisplayName, NomRefCache
  91
  92                                 Integer id = (Integer)rs.getObject("RECORD_NUMBER");
  93
  94                                 String preferredName = rs.getString("PreferredName");
  95                                 if (StringUtils.isBlank(preferredName)){
  96                                         logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD_NUMBER" + CdmUtils.Nz(id));
  97                                 }
  98
  99                                 Rank rank = Rank.SPECIES();
 100
 101                                 NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 102                                 NonViralName<?> name = parser.parseSimpleName(preferredName, NomenclaturalCode.ICBN, rank);
 103
 104                                 Taxon taxon = Taxon.NewInstance(name, sourceReference);
 105                                 Taxon parent = getParentTaxon(state, rs);
 106                                 classification.addParentChild(parent, taxon, null, null);
 107
 108                                 //author + publication
 109                                 makeAuthorAndPublication(state, rs, name);
 110                                 //source
 111                                 makeSource(state, taxon, id, NAMESPACE_SPECIES );
 112
 113                                 getTaxonService().saveOrUpdate(taxon);
 114                         }
 115
 116
 117                 } catch (Exception e) {
 118                         e.printStackTrace();
 119                         logger.error(e.getMessage());
 120                         state.setSuccess(false);
 121                         success = false;
 122                 }
 123                 return success;
 124         }
 125
 126
 127         private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {
 128                 Integer genusId = rs.getInt("PreferredNameFDCnumber");
 129
 130                 Taxon taxon = state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);
 131                 if (taxon == null){
 132                         logger.warn("Taxon not found for " + genusId);
 133                 }
 134                 return taxon;
 135         }
 136
 137         /* (non-Javadoc)
 138          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 139          */
 140         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 141                 String nameSpace;
 142                 Class cdmClass;
 143                 Set<String> idSet;
 144                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 145
 146                 try{
 147                         Set<String> taxonIdSet = new HashSet<String>();
 148                         while (rs.next()){
 149                                 handleForeignKey(rs, taxonIdSet,"PreferredNameFDCnumber" );
 150                         }
 151
 152                         //taxon map
 153                         nameSpace = NAMESPACE_GENERA;
 154                         cdmClass = TaxonBase.class;
 155                         idSet = taxonIdSet;
 156                         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 157                         result.put(nameSpace, taxonMap);
 158
 159                         //sourceReference
 160                         Reference<?> sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);
 161                         Map<String, Reference> referenceMap = new HashMap<String, Reference>();
 162                         referenceMap.put(SOURCE_REFERENCE, sourceReference);
 163                         result.put(NAMESPACE_REFERENCE, referenceMap);
 164
 165                 } catch (SQLException e) {
 166                         throw new RuntimeException(e);
 167                 }
 168                 return result;
 169         }
 170
 171
 172
 173         /* (non-Javadoc)
 174          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 175          */
 176         @Override
 177         protected boolean doCheck(IndexFungorumImportState state){
 178                 return true;
 179         }
 180
 181         /* (non-Javadoc)
 182          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 183          */
 184         protected boolean isIgnore(IndexFungorumImportState state){
 185                 return ! state.getConfig().isDoTaxa();
 186         }
 187
 188
 189
 190
 191
 192 }