cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelOccurrenceIO.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.io.berlinModel;
   5
   6 import java.sql.ResultSet;
   7 import java.sql.SQLException;
   8 import java.util.HashSet;
   9 import java.util.Set;
  10
  11 import org.apache.log4j.Logger;
  12 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.*;
  13 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  14 import eu.etaxonomy.cdm.api.service.ITaxonService;
  15 import eu.etaxonomy.cdm.io.source.Source;
  16 import eu.etaxonomy.cdm.model.common.Language;
  17 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  18 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  19 import eu.etaxonomy.cdm.model.description.TextData;
  20 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  21 import eu.etaxonomy.cdm.model.taxon.Taxon;
  22 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  23
  24
  25 /**
  26  * @author a.mueller
  27  *
  28  */
  29 public class BerlinModelOccurrenceIO {
  30         private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceIO.class);
  31
  32         private static int modCount = 10000;
  33
  34         public static boolean check(BerlinModelImportConfigurator bmiConfig){
  35                 boolean result = true;
  36                 logger.warn("Checking for Occurrence not yet implemented");
  37                 //result &= checkArticlesWithoutJournal(bmiConfig);
  38                 //result &= checkPartOfJournal(bmiConfig);
  39
  40                 return result;
  41         }
  42
  43         public static boolean invoke(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp,
  44                         MapWrapper<TaxonBase> taxonMap, MapWrapper<ReferenceBase> referenceMap){
  45
  46                 Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();
  47                 Source source = bmiConfig.getSource();
  48                 ITaxonService taxonService = cdmApp.getTaxonService();
  49
  50                 String dbAttrName;
  51                 String cdmAttrName;
  52
  53                 logger.info("start makeFacts ...");
  54
  55                 boolean delete = bmiConfig.isDeleteAll();
  56
  57                 try {
  58                         //get data from database
  59                         String strQuery =
  60                                         " SELECT xxx.*, PTaxon.RIdentifier as taxonId " +
  61                                         " FROM Fact INNER JOIN " +
  62                         " dbo.PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "+
  63                     " WHERE (1=1)";
  64                         ResultSet rs = source.getResultSet(strQuery) ;
  65
  66                         int i = 0;
  67                         //for each reference
  68                         while (rs.next()){
  69
  70                                 if ((i++ % modCount) == 0){ logger.info("Facts handled: " + (i-1));}
  71
  72                                 int occurrenceId = rs.getInt("occId");
  73                                 int taxonId = rs.getInt("taxonId");
  74                                 int factRefFk = rs.getInt("factRefFk");
  75                                 int categoryFk = rs.getInt("factCategoryFk");
  76
  77                                 TaxonBase taxonBase = taxonMap.get(taxonId);
  78
  79                                 if (taxonBase != null){
  80                                         Taxon taxon;
  81                                         if ( taxonBase instanceof Taxon ) {
  82                                                 taxon = (Taxon) taxonBase;
  83                                         }else{
  84                                                 logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
  85                                                 continue;
  86                                         }
  87
  88                                         TaxonDescription taxonDescription = TaxonDescription.NewInstance();
  89
  90                                         taxon.addDescription(taxonDescription);
  91
  92                                         //commonNames
  93                                         String commonNameString;
  94                                         if (taxon.getName() != null){
  95                                                 commonNameString = "Common " + taxon.getName().getTitleCache();
  96                                         }else{
  97                                                 commonNameString = "Common (null)";
  98                                         }
  99                                         Language language = bmiConfig.getFactLanguage();
 100                                         language = null;
 101                                         CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language);
 102                                         taxonDescription.addElement(commonName);
 103
 104
 105                                         //TODO
 106                                         //etc.
 107
 108                                         taxonStore.add(taxon);
 109                                 }else{
 110                                         //TODO
 111                                         logger.warn("Taxon for Fact " + occurrenceId + " does not exist in store");
 112                                 }
 113                                 //put
 114                         }
 115                         logger.info("Taxa to save: " + taxonStore.size());
 116                         taxonService.saveTaxonAll(taxonStore);
 117
 118                         logger.info("end makeFacts ...");
 119                         return true;
 120                 } catch (SQLException e) {
 121                         logger.error("SQLException:" +  e);
 122                         return false;
 123                 }
 124
 125         }
 126
 127
 128 }