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.erms.ErmsTransformer;
  26 import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
  27 import eu.etaxonomy.cdm.model.common.CdmBase;
  28 import eu.etaxonomy.cdm.model.common.Extension;
  29 import eu.etaxonomy.cdm.model.common.ExtensionType;
  30 import eu.etaxonomy.cdm.model.common.MarkerType;
  31 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  32 import eu.etaxonomy.cdm.model.name.NonViralName;
  33 import eu.etaxonomy.cdm.model.name.Rank;
  34 import eu.etaxonomy.cdm.model.reference.Reference;
  35 import eu.etaxonomy.cdm.model.taxon.Classification;
  36 import eu.etaxonomy.cdm.model.taxon.Taxon;
  37 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  38 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  39
  40
  41 /**
  42  * @author a.mueller
  43  * @created 27.02.2012
  44  */
  45 @Component
  46 public class IndexFungorumSpeciesImport  extends IndexFungorumImportBase {
  47         private static final Logger logger = Logger.getLogger(IndexFungorumSpeciesImport.class);
  48
  49         private static final String pluralString = "species";
  50         private static final String dbTableName = "[tblPESIfungi-IFdata]";
  51
  52         public IndexFungorumSpeciesImport(){
  53                 super(pluralString, dbTableName, null);
  54         }
  55
  56
  57
  58
  59         @Override
  60         protected String getIdQuery() {
  61                 String result = " SELECT RECORD_NUMBER FROM " + getTableName() +
  62                                 " ORDER BY PreferredName ";
  63                 return result;
  64         }
  65
  66
  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(IndexFungorumImportConfigurator config) {
  74                 String strRecordQuery =
  75                                 " SELECT DISTINCT distribution.PreferredNameFDCnumber, species.* , cl.PhylumName" +
  76                                 " FROM tblPESIfungi AS distribution RIGHT OUTER JOIN  dbo.[tblPESIfungi-IFdata] AS species ON distribution.PreferredNameIFnumber = species.RECORD_NUMBER " +
  77                                         " LEFT OUTER JOIN [tblPESIfungi-Classification] cl ON species.PreferredName   = cl.PreferredName " +
  78                                 " WHERE ( species.RECORD_NUMBER IN (" + ID_LIST_TOKEN + ") )" +
  79                         "";
  80                 return strRecordQuery;
  81         }
  82
  83
  84         @Override
  85         public boolean doPartition(ResultSetPartitioner partitioner, IndexFungorumImportState state) {
  86                 boolean success = true;
  87                 Reference<?> sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
  88                 ResultSet rs = partitioner.getResultSet();
  89
  90                 Classification classification = getClassification(state);
  91                 try {
  92                         while (rs.next()){
  93
  94                                 //DisplayName, NomRefCache -> don't use, created by Marc
  95
  96                                 Integer id = (Integer)rs.getObject("RECORD_NUMBER");
  97                                 String phylumName = rs.getString("PhylumName");
  98
  99                                 String preferredName = rs.getString("PreferredName");
 100                                 if (StringUtils.isBlank(preferredName)){
 101                                         logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD_NUMBER" + CdmUtils.Nz(id));
 102                                 }
 103
 104                                 Rank rank = Rank.SPECIES();
 105
 106                                 NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 107                                 NonViralName<?> name = parser.parseSimpleName(preferredName, NomenclaturalCode.ICBN, rank);
 108
 109                                 Taxon taxon = Taxon.NewInstance(name, sourceReference);
 110                                 Taxon parent = getParentTaxon(state, rs);
 111                                 classification.addParentChild(parent, taxon, null, null);
 112
 113                                 //author + publication
 114                                 makeAuthorAndPublication(state, rs, name);
 115                                 //source
 116                                 makeSource(state, taxon, id, NAMESPACE_SPECIES );
 117
 118                                 //fossil
 119                                 if (FOSSIL_FUNGI.equalsIgnoreCase(phylumName)){
 120                                         ExtensionType fossilExtType = getExtensionType(state, ErmsTransformer.uuidFossilStatus, "fossil status", "fossil status", "fos. stat.");
 121                                         Extension.NewInstance(taxon, PesiTransformer.STR_FOSSIL_ONLY, fossilExtType);
 122                                 }
 123                                 //save
 124                                 getTaxonService().saveOrUpdate(taxon);
 125                         }
 126
 127
 128                 } catch (Exception e) {
 129                         e.printStackTrace();
 130                         logger.error(e.getMessage());
 131                         state.setSuccess(false);
 132                         success = false;
 133                 }
 134                 return success;
 135         }
 136
 137
 138         private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {
 139                 Integer genusId = rs.getInt("PreferredNameFDCnumber");
 140
 141                 Taxon taxon = state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);
 142                 if (taxon == null){
 143                         logger.warn("Taxon not found for " + genusId);
 144                 }
 145                 return taxon;
 146         }
 147
 148         /* (non-Javadoc)
 149          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 150          */
 151         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 152                 String nameSpace;
 153                 Class cdmClass;
 154                 Set<String> idSet;
 155                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 156
 157                 try{
 158                         Set<String> taxonIdSet = new HashSet<String>();
 159                         while (rs.next()){
 160                                 handleForeignKey(rs, taxonIdSet,"PreferredNameFDCnumber" );
 161                         }
 162
 163                         //taxon map
 164                         nameSpace = NAMESPACE_GENERA;
 165                         cdmClass = TaxonBase.class;
 166                         idSet = taxonIdSet;
 167                         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 168                         result.put(nameSpace, taxonMap);
 169
 170                         //sourceReference
 171                         Reference<?> sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);
 172                         Map<String, Reference> referenceMap = new HashMap<String, Reference>();
 173                         referenceMap.put(SOURCE_REFERENCE, sourceReference);
 174                         result.put(NAMESPACE_REFERENCE, referenceMap);
 175
 176                 } catch (SQLException e) {
 177                         throw new RuntimeException(e);
 178                 }
 179                 return result;
 180         }
 181
 182
 183
 184         /* (non-Javadoc)
 185          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 186          */
 187         @Override
 188         protected boolean doCheck(IndexFungorumImportState state){
 189                 return true;
 190         }
 191
 192         /* (non-Javadoc)
 193          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 194          */
 195         protected boolean isIgnore(IndexFungorumImportState state){
 196                 return ! state.getConfig().isDoTaxa();
 197         }
 198
 199
 200
 201
 202
 203 }