cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaAdditionalTaxonDataImport.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.faunaEuropaea;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Set;
  17 import java.util.UUID;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21 import org.springframework.transaction.TransactionStatus;
  22
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.io.common.Source;
  25 import eu.etaxonomy.cdm.model.common.CdmBase;
  26 import eu.etaxonomy.cdm.model.name.NonViralName;
  27 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  28 import eu.etaxonomy.cdm.model.taxon.Taxon;
  29 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  30
  31
  32 /**
  33  * @author a.babadshanjan
  34  * @created 21.08.2010
  35  * @version 1.0
  36  */
  37 @Component
  38 public class FaunaEuropaeaAdditionalTaxonDataImport extends FaunaEuropaeaImportBase  {
  39
  40         private static final Logger logger = Logger.getLogger(FaunaEuropaeaAdditionalTaxonDataImport.class);
  41         private static final String parentPluralString = "Synonyms";
  42         private static final String pluralString = "InfraGenericEpithets";
  43         private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database
  44
  45         /* (non-Javadoc)
  46          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  47          */
  48         @Override
  49         protected boolean doCheck(FaunaEuropaeaImportState state) {
  50                 boolean result = true;
  51                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  52                 logger.warn("Checking for Taxa not yet fully implemented");
  53                 result &= checkTaxonStatus(fauEuConfig);
  54
  55                 return result;
  56         }
  57
  58         /* (non-Javadoc)
  59          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  60          */
  61         protected boolean isIgnore(FaunaEuropaeaImportState state) {
  62                 return ! state.getConfig().isDoTaxa();
  63         }
  64
  65         private boolean checkTaxonStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
  66                 boolean result = true;
  67 //              try {
  68                         Source source = fauEuConfig.getSource();
  69                         String sqlStr = "";
  70                         ResultSet rs = source.getResultSet(sqlStr);
  71                         return result;
  72 //              } catch (SQLException e) {
  73 //                      e.printStackTrace();
  74 //                      return false;
  75 //              }
  76         }
  77
  78         /**
  79          * Import taxa from FauEU DB
  80          */
  81         protected void doInvoke(FaunaEuropaeaImportState state) {
  82
  83                 if(logger.isInfoEnabled()) {
  84                         logger.info("Started creating " + pluralString + "...");
  85                 }
  86
  87                 processAdditionalInfraGenericEpithets(state);
  88
  89                 logger.info("The End is Nigh... " + pluralString + "...");
  90                 return;
  91         }
  92
  93         /**
  94          *
  95          * @param state
  96          * @return
  97          */
  98         private void processAdditionalInfraGenericEpithets(FaunaEuropaeaImportState state) {
  99                 int count = 0;
 100                 int pageSize = 1000;
 101                 Set<UUID> uuidSet = new HashSet<UUID>();
 102                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
 103                 ICdmDataSource destination = fauEuConfig.getDestination();
 104                 TransactionStatus txStatus = null;
 105                 List<TaxonNameBase> taxonNames = null;
 106                 txStatus = startTransaction(false);
 107
 108                 String selectQuery = "SELECT t.uuid from TaxonNameBase t INNER JOIN " +
 109                                 "TaxonNameBase t2 ON t.GenusOrUninomial = t2.GenusOrUninomial AND t.SpecificEpithet = t2.SpecificEpithet " +
 110                                 "WHERE t.InfraGenericEpithet IS NULL AND t.rank_id = 764 AND t2.rank_id = 766 AND t2.InfraGenericEpithet IS NOT NULL";
 111
 112                 logger.info("Retrieving TaxonNames...");
 113
 114                 ResultSet resultSet;
 115                 try {
 116                         resultSet = destination.executeQuery(selectQuery);
 117
 118                         // Collect UUIDs
 119                         while (resultSet.next()) {
 120                                 uuidSet.add(UUID.fromString(resultSet.getString("UUID")));
 121                         }
 122                 } catch (SQLException e) {
 123                         logger.error("An error occured: ", e);
 124                 }
 125
 126                 // Fetch TaxonName objects for UUIDs
 127                 taxonNames = getNameService().find(uuidSet);
 128
 129                 for (TaxonNameBase taxonName : taxonNames) {
 130
 131                         // Check whether its taxonName has an infraGenericEpithet
 132                         if (taxonName != null && (taxonName.isInstanceOf(NonViralName.class))) {
 133                                 NonViralName targetNonViralName = CdmBase.deproxy(taxonName, NonViralName.class);
 134                                 String infraGenericEpithet = targetNonViralName.getInfraGenericEpithet();
 135                                 if (infraGenericEpithet == null) {
 136                                         String genusOrUninomial = targetNonViralName.getGenusOrUninomial();
 137                                         String specificEpithet = targetNonViralName.getSpecificEpithet();
 138                                         List<TaxonBase> foundTaxa = getTaxonService().listTaxaByName(Taxon.class, genusOrUninomial, "*", specificEpithet,
 139                                                         "*", null, pageSize, 1);
 140                                         if (foundTaxa.size() == 1) {
 141                                                 // one matching Taxon found
 142                                                 TaxonBase taxon = foundTaxa.iterator().next();
 143                                                 if (taxon != null) {
 144                                                         TaxonNameBase name = taxon.getName();
 145                                                         if (name != null && name.isInstanceOf(NonViralName.class)) {
 146                                                                 NonViralName nonViralName = CdmBase.deproxy(name, NonViralName.class);
 147                                                                 infraGenericEpithet = nonViralName.getInfraGenericEpithet();
 148
 149                                                                 // set infraGenericEpithet
 150 //                                                                      targetNonViralName.setInfraGenericEpithet(infraGenericEpithet);
 151                                                                 logger.info("Added an InfraGenericEpithet to this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
 152                                                                 count++;
 153                                                         }
 154                                                 }
 155                                         } else if (foundTaxa.size() > 1) {
 156                                                 logger.warn("Multiple taxa match search criteria: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
 157                                                 for (TaxonBase foundTaxon : foundTaxa) {
 158                                                         logger.warn(foundTaxon.getUuid() + ", " + foundTaxon.getTitleCache());
 159                                                 }
 160                                         } else if (foundTaxa.size() == 0) {
 161 //                                                      logger.error("No matches for search criteria: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
 162                                         }
 163                                 }
 164
 165                         }
 166                 }
 167
 168                 // Commit transaction
 169                 commitTransaction(txStatus);
 170                 logger.info("Committed transaction.");
 171
 172                 return;
 173         }
 174
 175 }