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.Map;
  10 import java.util.Set;
  11
  12 import org.apache.log4j.Logger;
  13 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.*;
  14 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  15 import eu.etaxonomy.cdm.api.service.ITaxonService;
  16 import eu.etaxonomy.cdm.io.common.ICdmIO;
  17 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  18 import eu.etaxonomy.cdm.io.common.MapWrapper;
  19 import eu.etaxonomy.cdm.io.common.Source;
  20 import eu.etaxonomy.cdm.model.common.CdmBase;
  21 import eu.etaxonomy.cdm.model.common.Language;
  22 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  23 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  24 import eu.etaxonomy.cdm.model.description.TextData;
  25 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  26 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  27 import eu.etaxonomy.cdm.model.taxon.Taxon;
  28 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  29
  30
  31 /**
  32  * @author a.mueller
  33  *
  34  */
  35 public class BerlinModelOccurrenceIO  extends BerlinModelIOBase {
  36         private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceIO.class);
  37
  38         private static int modCount = 10000;
  39
  40         public BerlinModelOccurrenceIO(){
  41                 super();
  42         }
  43
  44         /* (non-Javadoc)
  45          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  46          */
  47         @Override
  48         protected boolean doCheck(IImportConfigurator config){
  49                 boolean result = true;
  50                 logger.warn("Checking for Occurrence not yet implemented");
  51                 //result &= checkArticlesWithoutJournal(bmiConfig);
  52                 //result &= checkPartOfJournal(bmiConfig);
  53
  54                 return result;
  55         }
  56
  57         /* (non-Javadoc)
  58          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  59          */
  60         @Override
  61         protected boolean doInvoke(IImportConfigurator config, CdmApplicationController cdmApp,
  62                         Map<String, MapWrapper<? extends CdmBase>> stores){
  63
  64                 MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
  65                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
  66                 BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
  67
  68                 if (true){
  69                         return false;
  70                 }
  71
  72
  73
  74
  75
  76
  77
  78
  79                 Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();
  80                 Source source = bmiConfig.getSource();
  81                 ITaxonService taxonService = cdmApp.getTaxonService();
  82
  83                 String dbAttrName;
  84                 String cdmAttrName;
  85
  86                 logger.info("start makeFacts ...");
  87
  88                 boolean delete = bmiConfig.isDeleteAll();
  89
  90                 try {
  91                         //get data from database
  92                         String strQuery =
  93                                         " SELECT xxx.*, PTaxon.RIdentifier as taxonId " +
  94                                         " FROM Fact INNER JOIN " +
  95                         " dbo.PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "+
  96                     " WHERE (1=1)";
  97                         ResultSet rs = source.getResultSet(strQuery) ;
  98
  99                         int i = 0;
 100                         //for each reference
 101                         while (rs.next()){
 102
 103                                 if ((i++ % modCount) == 0){ logger.info("Facts handled: " + (i-1));}
 104
 105                                 int occurrenceId = rs.getInt("occId");
 106                                 int taxonId = rs.getInt("taxonId");
 107                                 int factRefFk = rs.getInt("factRefFk");
 108                                 int categoryFk = rs.getInt("factCategoryFk");
 109
 110                                 TaxonBase taxonBase = taxonMap.get(taxonId);
 111
 112                                 if (taxonBase != null){
 113                                         Taxon taxon;
 114                                         if ( taxonBase instanceof Taxon ) {
 115                                                 taxon = (Taxon) taxonBase;
 116                                         }else{
 117                                                 logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
 118                                                 continue;
 119                                         }
 120
 121                                         TaxonDescription taxonDescription = TaxonDescription.NewInstance();
 122
 123                                         taxon.addDescription(taxonDescription);
 124
 125                                         //commonNames
 126                                         String commonNameString;
 127                                         if (taxon.getName() != null){
 128                                                 commonNameString = "Common " + taxon.getName().getTitleCache();
 129                                         }else{
 130                                                 commonNameString = "Common (null)";
 131                                         }
 132                                         Language language = bmiConfig.getFactLanguage();
 133                                         language = null;
 134                                         CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language);
 135                                         taxonDescription.addElement(commonName);
 136
 137
 138                                         //TODO
 139                                         //etc.
 140
 141                                         taxonStore.add(taxon);
 142                                 }else{
 143                                         //TODO
 144                                         logger.warn("Taxon for Fact " + occurrenceId + " does not exist in store");
 145                                 }
 146                                 //put
 147                         }
 148                         logger.info("Taxa to save: " + taxonStore.size());
 149                         taxonService.saveTaxonAll(taxonStore);
 150
 151                         logger.info("end makeFacts ...");
 152                         return true;
 153                 } catch (SQLException e) {
 154                         logger.error("SQLException:" +  e);
 155                         return false;
 156                 }
 157
 158         }
 159
 160         /* (non-Javadoc)
 161          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 162          */
 163         protected boolean isIgnore(IImportConfigurator config){
 164                 return ! config.isDoOccurrence();
 165         }
 166
 167
 168 }