cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonNameRelationImport.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.berlinModel;
  11
  12 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_HAS_SAME_TYPE_AS;
  13 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_BASIONYM_FOR;
  14 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_CONSERVED_TYPE_OF;
  15 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FEMALE_PARENT_OF;
  16 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FIRST_PARENT_OF;
  17 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_HOMONYM_OF;
  18 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LECTOTYPE_OF;
  19 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_MALE_PARENT_OF;
  20 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
  21 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REJECTED_TYPE_OF;
  22 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REPLACED_SYNONYM_FOR;
  23 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_SECOND_PARENT_OF;
  24 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF;
  25 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_TYPE_NOT_DESIGNATED;
  26
  27 import java.sql.ResultSet;
  28 import java.sql.SQLException;
  29 import java.util.HashSet;
  30 import java.util.Map;
  31 import java.util.Set;
  32
  33 import org.apache.log4j.Logger;
  34 import org.springframework.stereotype.Component;
  35
  36 import eu.etaxonomy.cdm.io.common.ICdmIO;
  37 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  38 import eu.etaxonomy.cdm.io.common.MapWrapper;
  39 import eu.etaxonomy.cdm.io.common.Source;
  40 import eu.etaxonomy.cdm.model.common.CdmBase;
  41 import eu.etaxonomy.cdm.model.name.BotanicalName;
  42 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  43 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  44 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  45 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  46 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  47
  48 /**
  49  * @author a.mueller
  50  * @created 20.03.2008
  51  * @version 1.0
  52  */
  53 @Component
  54 public class BerlinModelTaxonNameRelationImport extends BerlinModelImportBase {
  55         private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameRelationImport.class);
  56
  57         private static int modCount = 5000;
  58
  59         public BerlinModelTaxonNameRelationImport(){
  60                 super();
  61         }
  62
  63         /* (non-Javadoc)
  64          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  65          */
  66         @Override
  67         protected boolean doCheck(IImportConfigurator config){
  68                 boolean result = true;
  69                 logger.warn("Checking for TaxonNameRelations not yet implemented");
  70                 //result &= checkArticlesWithoutJournal(bmiConfig);
  71                 //result &= checkPartOfJournal(bmiConfig);
  72
  73                 return result;
  74         }
  75
  76         /* (non-Javadoc)
  77          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  78          */
  79         @Override
  80         protected boolean doInvoke(IImportConfigurator config,
  81                         Map<String, MapWrapper<? extends CdmBase>> stores){
  82
  83                 MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)stores.get(ICdmIO.TAXONNAME_STORE);
  84                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
  85
  86                 Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>();
  87                 BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
  88                 Source source = bmiConfig.getSource();
  89
  90                 logger.info("start makeNameRelationships ...");
  91
  92                 try {
  93                         //get data from database
  94                         String strQuery =
  95                                         " SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
  96                                         " FROM Name as FromName INNER JOIN " +
  97                         " RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
  98                         " Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
  99                         " RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
 100                     " WHERE (1=1)";
 101                         ResultSet rs = source.getResultSet(strQuery) ;
 102
 103                         int i = 0;
 104                         //for each reference
 105                         while (rs.next()){
 106
 107                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelName handled: " + (i-1));}
 108
 109                                 int relNameId = rs.getInt("RelNameId");
 110                                 int name1Id = rs.getInt("name1Id");
 111                                 int name2Id = rs.getInt("name2Id");
 112                                 int relRefFk = rs.getInt("refFk");
 113                                 String details = rs.getString("details");
 114                                 int relQualifierFk = rs.getInt("relNameQualifierFk");
 115
 116                                 TaxonNameBase nameFrom = taxonNameMap.get(name1Id);
 117                                 TaxonNameBase nameTo = taxonNameMap.get(name2Id);
 118
 119                                 ReferenceBase citation = referenceMap.get(relRefFk);
 120                                 //TODO (preliminaryFlag = true testen
 121                                 String microcitation = details;
 122                                 String rule = null;  //TODO
 123
 124                                 if (nameFrom != null && nameTo != null){
 125                                         if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
 126                                                 nameTo.addBasionym(nameFrom, citation, microcitation, rule);
 127                                         }else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
 128                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
 129                                         }else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
 130                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule) ;
 131                                         }else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
 132                                                 nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());//nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), rule) ;
 133                                         }else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF ||  relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF || relQualifierFk == NAME_REL_IS_LECTOTYPE_OF || relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED ){
 134                                                 //TODO
 135                                                 String originalNameString = null;
 136                                                 boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF);
 137                                                 boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF);
 138                                                 boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF);
 139                                                 boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED);
 140
 141                                                 //TODO addToAllNames true or false?
 142                                                 nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, isRejectedType, isConservedType, isLectoType, isNotDesignated, false);
 143
 144                                         }else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
 145                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule) ;
 146                                         }else if (relQualifierFk == NAME_REL_IS_FIRST_PARENT_OF || relQualifierFk == NAME_REL_IS_SECOND_PARENT_OF || relQualifierFk == NAME_REL_IS_FEMALE_PARENT_OF || relQualifierFk == NAME_REL_IS_MALE_PARENT_OF){
 147                                                 //HybridRelationships
 148                                                 if (! (nameTo instanceof BotanicalName) || ! (nameFrom instanceof BotanicalName)){
 149                                                         logger.warn("HybridrelationshipNames ("+name1Id +"," + name2Id +") must be of type BotanicalName but are not");
 150                                                 }
 151                                                 try {
 152                                                         HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk);
 153                                                         BotanicalName parent = (BotanicalName)nameFrom;
 154                                                         BotanicalName child = (BotanicalName)nameTo;
 155
 156                                                         //TODO bug when trying to persist
 157                                                         //parent.addHybridChild(child, hybridRelType, rule);
 158                                                         logger.warn("HybridRelationships not yet implemented");
 159
 160                                                         //TODO reference
 161                                                 } catch (UnknownCdmTypeException e) {
 162                                                         //TODO
 163                                                         logger.warn(e);
 164                                                 }
 165                                         }else {
 166                                                 //TODO
 167                                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 168                                         }
 169                                         nameStore.add(nameFrom);
 170
 171                                         //TODO
 172                                         //ID
 173                                         //etc.
 174                                 }else{
 175                                         //TODO
 176                                         if (nameFrom == null){
 177                                                  logger.warn("from TaxonName for RelName (" + relNameId + ") does not exist in store");
 178                                         }
 179                                         if (nameTo == null){
 180                                                 logger.warn("to TaxonNames for RelName (" + relNameId + ") does not exist in store");
 181                                         }
 182                                 }
 183                         }
 184                         logger.info("TaxonName to save: " + nameStore.size());
 185                         getNameService().saveTaxonNameAll(nameStore);
 186
 187                         logger.info("end makeNameRelationships ...");
 188                         return true;
 189                 } catch (SQLException e) {
 190                         logger.error("SQLException:" +  e);
 191                         return false;
 192                 }
 193
 194         }
 195
 196         /* (non-Javadoc)
 197          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 198          */
 199         protected boolean isIgnore(IImportConfigurator config){
 200                 return ! config.isDoRelNames();
 201         }
 202
 203 }