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

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.io.berlinModel;
   5
   6 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_ACCEPTED;
   7 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_SYNONYM;
   8 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_PRO_PARTE_SYN;
   9 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_PARTIAL_SYN;
  10
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.Map;
  15
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  19 import eu.etaxonomy.cdm.api.service.ITaxonService;
  20 import eu.etaxonomy.cdm.io.common.ICdmIO;
  21 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  22 import eu.etaxonomy.cdm.io.common.ImportHelper;
  23 import eu.etaxonomy.cdm.io.common.MapWrapper;
  24 import eu.etaxonomy.cdm.io.common.Source;
  25 import eu.etaxonomy.cdm.model.common.CdmBase;
  26 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  27 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  28 import eu.etaxonomy.cdm.model.taxon.Synonym;
  29 import eu.etaxonomy.cdm.model.taxon.Taxon;
  30 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  31
  32
  33 /**
  34  * @author a.mueller
  35  *
  36  */
  37 public class BerlinModelTaxonIO  extends BerlinModelIOBase  {
  38         private static final Logger logger = Logger.getLogger(BerlinModelTaxonIO.class);
  39
  40         private int modCount = 30000;
  41
  42         public BerlinModelTaxonIO(){
  43                 super();
  44         }
  45
  46         /* (non-Javadoc)
  47          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  48          */
  49         @Override
  50         protected boolean doCheck(IImportConfigurator config){
  51                 boolean result = true;
  52                 BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
  53                 logger.warn("Checking for Taxa not yet fully implemented");
  54                 result &= checkTaxonStatus(bmiConfig);
  55                 //result &= checkArticlesWithoutJournal(bmiConfig);
  56
  57                 return result;
  58         }
  59
  60         private boolean checkTaxonStatus(BerlinModelImportConfigurator bmiConfig){
  61                 try {
  62                         boolean result = true;
  63                         Source source = bmiConfig.getSource();
  64                         String strSQL = " SELECT RelPTaxon.RelQualifierFk, RelPTaxon.relPTaxonId, PTaxon.PTNameFk, PTaxon.PTRefFk, PTaxon_1.PTNameFk AS Expr1, PTaxon.RIdentifier, PTaxon_1.RIdentifier AS Expr3, Name.FullNameCache "  +
  65                                 " FROM RelPTaxon " +
  66                                         " INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
  67                                         " INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk  " +
  68                                         " INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
  69                                 " WHERE (dbo.PTaxon.StatusFk = 1) AND ((RelPTaxon.RelQualifierFk = 7) OR (RelPTaxon.RelQualifierFk = 6) OR (RelPTaxon.RelQualifierFk = 2)) ";
  70                         ResultSet rs = source.getResultSet(strSQL);
  71                         boolean firstRow = true;
  72                         int i = 0;
  73                         while (rs.next()){
  74                                 i++;
  75                                 if (firstRow){
  76                                         System.out.println("========================================================");
  77                                         logger.warn("There are taxa that have a 'is synonym of' - relationship but having taxon status 'accepted'!");
  78                                         System.out.println("========================================================");
  79                                 }
  80                                 int rIdentifier = rs.getInt("RIdentifier");
  81                                 int nameFk = rs.getInt("PTNameFk");
  82                                 int refFk = rs.getInt("PTRefFk");
  83                                 int relPTaxonId = rs.getInt("relPTaxonId");
  84                                 String taxonName = rs.getString("FullNameCache");
  85
  86                                 System.out.println("RIdentifier:" + rIdentifier + "\n  name: " + nameFk +
  87                                                 "\n  taxonName: " + taxonName + "\n  refId: " + refFk + "\n  RelPTaxonId: " + relPTaxonId );
  88                                 result = firstRow = false;
  89                         }
  90                         if (i > 0){
  91                                 System.out.println(" ");
  92                         }
  93
  94                         return result;
  95                 } catch (SQLException e) {
  96                         e.printStackTrace();
  97                         return false;
  98                 }
  99         }
 100
 101         /* (non-Javadoc)
 102          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
 103          */
 104         @Override
 105         protected boolean doInvoke(IImportConfigurator config, CdmApplicationController cdmApp,
 106                         Map<String, MapWrapper<? extends CdmBase>> stores){
 107
 108                 MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)stores.get(ICdmIO.TAXONNAME_STORE);
 109                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
 110                 MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_STORE);
 111                 MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
 112
 113                 BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
 114                 Source source = bmiConfig.getSource();
 115                 String dbAttrName;
 116                 String cdmAttrName;
 117
 118                 logger.info("start makeTaxa ...");
 119
 120                 ITaxonService taxonService = cdmApp.getTaxonService();
 121
 122                 try {
 123                         //get data from database
 124                         String strQuery =
 125                                         " SELECT * " +
 126                                         " FROM PTaxon " +
 127                                         " WHERE (1=1)";
 128
 129                         ResultSet rs = source.getResultSet(strQuery) ;
 130
 131                         int i = 0;
 132                         //for each reference
 133                         while (rs.next()){
 134
 135                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
 136
 137                                 //create TaxonName element
 138                                 int taxonId = rs.getInt("RIdentifier");
 139                                 int statusFk = rs.getInt("statusFk");
 140
 141                                 int nameFk = rs.getInt("PTNameFk");
 142                                 int refFk = rs.getInt("PTRefFk");
 143                                 String doubtful = rs.getString("DoubtfulFlag");
 144
 145                                 TaxonNameBase taxonName = null;
 146                                 if (taxonNameMap != null){
 147                                         taxonName  = taxonNameMap.get(nameFk);
 148                                 }
 149
 150                                 ReferenceBase reference = null;
 151                                 if (referenceMap != null){
 152                                         reference = referenceMap.get(refFk);
 153                                         if (reference == null){
 154                                                 reference = nomRefMap.get(refFk);
 155                                         }
 156                                 }
 157
 158                                 if(! config.isIgnoreNull()){
 159                                         if (taxonName == null ){
 160                                                 logger.warn("TaxonName belonging to taxon (RIdentifier = " + taxonId + ") could not be found in store. Taxon will not be transported");
 161                                                 continue; //next taxon
 162                                         }else if (reference == null ){
 163                                                 logger.warn("Reference belonging to taxon could not be found in store. Taxon will not be imported");
 164                                                 continue; //next taxon
 165                                         }
 166                                 }
 167                                 TaxonBase taxonBase;
 168                                 Synonym synonym;
 169                                 Taxon taxon;
 170                                 try {
 171                                         logger.debug(statusFk);
 172                                         if (statusFk == T_STATUS_ACCEPTED){
 173                                                 taxon = Taxon.NewInstance(taxonName, reference);
 174                                                 taxonBase = taxon;
 175                                         }else if (statusFk == T_STATUS_SYNONYM || statusFk == T_STATUS_PRO_PARTE_SYN || statusFk == T_STATUS_PARTIAL_SYN){
 176                                                 synonym = Synonym.NewInstance(taxonName, reference);
 177                                                 taxonBase = synonym;
 178                                                 if (statusFk == T_STATUS_PRO_PARTE_SYN){
 179                                                         bmiConfig.addProParteSynonym(synonym);
 180                                                 }
 181                                                 if (statusFk == T_STATUS_PARTIAL_SYN){
 182                                                         bmiConfig.addPartialSynonym(synonym);
 183                                                 }
 184                                         }else{
 185                                                 logger.warn("TaxonStatus " + statusFk + " not yet implemented. Taxon (RIdentifier = " + taxonId + ") left out.");
 186                                                 continue;
 187                                         }
 188
 189                                         //TODO
 190 //                                              dbAttrName = "Detail";
 191 //                                              cdmAttrName = "Micro";
 192 //                                              ImportHelper.addStringValue(rs, taxonBase, dbAttrName, cdmAttrName);
 193
 194                                         if (doubtful.equals("a")){
 195                                                 taxonBase.setDoubtful(false);
 196                                         }else if(doubtful.equals("d")){
 197                                                 taxonBase.setDoubtful(true);
 198                                         }else if(doubtful.equals("i")){
 199                                                 //TODO
 200                                                 logger.warn("Doubtful = i (inactivated) not yet implemented. Doubtful set to false");
 201                                         }
 202
 203                                         //nameId
 204                                         ImportHelper.setOriginalSource(taxonBase, bmiConfig.getSourceReference(), taxonId);
 205
 206
 207                                         //TODO
 208                                         //
 209                                         //Created
 210                                         //Note
 211                                         //ALL
 212
 213                                         taxonMap.put(taxonId, taxonBase);
 214                                 } catch (Exception e) {
 215                                         logger.warn("An exception occurred when creating taxon with id " + taxonId + ". Taxon could not be saved.");
 216                                 }
 217                         }
 218                         //invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap);
 219                         logger.info("saving taxa ...");
 220                         taxonService.saveTaxonAll(taxonMap.objects());
 221
 222                         logger.info("end makeTaxa ...");
 223
 224                         return true;
 225                 } catch (SQLException e) {
 226                         logger.error("SQLException:" +  e);
 227                         return false;
 228                 }
 229
 230         }
 231
 232         /* (non-Javadoc)
 233          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 234          */
 235         protected boolean isIgnore(IImportConfigurator config){
 236                 return ! config.isDoTaxa();
 237         }
 238
 239 }