app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelNameStatusImport.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.in;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.commons.lang.StringUtils;
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelNameStatusImportValidator;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  26 import eu.etaxonomy.cdm.io.common.IOValidator;
  27 import eu.etaxonomy.cdm.io.common.ImportHelper;
  28 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  29 import eu.etaxonomy.cdm.model.agent.Person;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.common.Marker;
  32 import eu.etaxonomy.cdm.model.common.MarkerType;
  33 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  34 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  35 import eu.etaxonomy.cdm.model.reference.Reference;
  36 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  37
  38 /**
  39  * @author a.mueller
  40  * @created 20.03.2008
  41  * @version 1.0
  42  */
  43 @Component
  44 public class BerlinModelNameStatusImport extends BerlinModelImportBase {
  45         private static final Logger logger = Logger.getLogger(BerlinModelNameStatusImport.class);
  46
  47         private int modCount = 5000;
  48         private static final String pluralString = "nomenclatural status";
  49         private static final String dbTableName = "NomStatusRel";
  50
  51
  52         public BerlinModelNameStatusImport(){
  53                 super(dbTableName, pluralString);
  54         }
  55
  56
  57
  58         /* (non-Javadoc)
  59          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  60          */
  61         @Override
  62         protected String getIdQuery(BerlinModelImportState state) {
  63                 String result =  " SELECT RIdentifier FROM " + getTableName();
  64
  65                 if (StringUtils.isNotEmpty(state.getConfig().getNameIdTable())){
  66                         result += " WHERE nameFk IN (SELECT NameId FROM " + state.getConfig().getNameIdTable() + ")";
  67                 }
  68                 return result;
  69         }
  70
  71
  72
  73         /* (non-Javadoc)
  74          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  75          */
  76         @Override
  77         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  78                 String strQuery =
  79                         " SELECT NomStatusRel.*, NomStatus.NomStatus, RefDetail.Details " +
  80                         " FROM NomStatusRel INNER JOIN " +
  81                 " NomStatus ON NomStatusRel.NomStatusFk = NomStatus.NomStatusId " +
  82                 " LEFT OUTER JOIN RefDetail ON NomStatusRel.NomStatusRefDetailFk = RefDetail.RefDetailId AND " +
  83                 " NomStatusRel.NomStatusRefFk = RefDetail.RefFk " +
  84             " WHERE (RIdentifier IN (" + ID_LIST_TOKEN + "))";
  85                 return strQuery;
  86         }
  87
  88         /* (non-Javadoc)
  89          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
  90          */
  91         public boolean doPartition(ResultSetPartitioner partitioner,BerlinModelImportState state) {
  92                 boolean success = true;
  93                 String dbAttrName;
  94                 String cdmAttrName;
  95
  96                 Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
  97                 BerlinModelImportConfigurator config = state.getConfig();
  98                 Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
  99
 100                 ResultSet rs = partitioner.getResultSet();
 101                 try {
 102                         //get data from database
 103
 104                         int i = 0;
 105                         //for each reference
 106                         while (rs.next()){
 107
 108                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("NomStatus handled: " + (i-1));}
 109
 110                                 int nomStatusRelId;
 111                                 try {
 112                                         nomStatusRelId = rs.getInt("RIdentifier");
 113                                 } catch (Exception e) {  //RIdentifier does not exist in BM database
 114                                         nomStatusRelId = -1;
 115                                 }
 116                                 int nomStatusFk = rs.getInt("NomStatusFk");
 117                                 int nameId = rs.getInt("nameFk");
 118
 119                                 boolean doubtful = rs.getBoolean("DoubtfulFlag");
 120                                 String nomStatusLabel = rs.getString("NomStatus");
 121
 122                                 TaxonNameBase taxonName = nameMap.get(String.valueOf(nameId));
 123                                 //TODO doubtful
 124
 125                                 if (taxonName != null ){
 126                                         try{
 127                                                 NomenclaturalStatus nomStatus = BerlinModelTransformer.nomStatusFkToNomStatus(nomStatusFk, nomStatusLabel);
 128                                                 if (nomStatus == null){
 129                                                         String message = "Nomenclatural status could not be defined for %s ; %s";
 130                                                         message = String.format(message, nomStatusFk, nomStatusLabel);
 131                                                         logger.warn(message);
 132                                                         success = false;
 133                                                         continue;
 134                                                 }else{
 135                                                         if (nomStatus.getType() == null){
 136                                                                 String message = "Nomenclatural status type could not be defined for %s ; %s";
 137                                                                 message = String.format(message, nomStatusFk, nomStatusLabel);
 138                                                                 logger.warn(message);
 139                                                                 success = false;
 140                                                                 continue;
 141                                                         }else if(nomStatus.getType().getId() == 0){
 142                                                                 getTermService().save(nomStatus.getType());
 143                                                         }
 144                                                 }
 145
 146                                                 //reference
 147                                                 makeReference(config, nomStatus, nameId, rs, partitioner);
 148
 149                                                 //Details
 150                                                 dbAttrName = "details";
 151                                                 cdmAttrName = "citationMicroReference";
 152                                                 success &= ImportHelper.addStringValue(rs, nomStatus, dbAttrName, cdmAttrName, true);
 153
 154                                                 //doubtful
 155                                                 if (doubtful){
 156                                                         nomStatus.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), true));
 157                                                 }
 158                                                 taxonName.addStatus(nomStatus);
 159                                                 namesToSave.add(taxonName);
 160                                         }catch (UnknownCdmTypeException e) {
 161                                                 logger.warn("NomStatusType " + nomStatusFk + " not yet implemented");
 162                                                 success = false;
 163                                         }
 164                                         //TODO
 165                                         //ID
 166                                         //etc.
 167                                 }else{
 168                                         logger.warn("TaxonName for NomStatusRel (" + nomStatusRelId + ") does not exist in store");
 169                                         success = false;
 170                                 }
 171                         }
 172                         logger.info("TaxonNames to save: " + namesToSave.size());
 173                         getNameService().save(namesToSave);
 174
 175                         return success;
 176                 } catch (SQLException e) {
 177                         logger.error("SQLException:" +  e);
 178                         return false;
 179                 }
 180
 181         }
 182
 183         /* (non-Javadoc)
 184          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 185          */
 186         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 187                 String nameSpace;
 188                 Class cdmClass;
 189                 Set<String> idSet;
 190                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 191
 192                 try{
 193                         Set<String> nameIdSet = new HashSet<String>();
 194                         Set<String> referenceIdSet = new HashSet<String>();
 195                         Set<String> refDetailIdSet = new HashSet<String>();
 196                         while (rs.next()){
 197                                 handleForeignKey(rs, nameIdSet, "nameFk");
 198                                 handleForeignKey(rs, referenceIdSet, "NomStatusRefFk");
 199                                 handleForeignKey(rs, refDetailIdSet, "NomStatusRefDetailFk");
 200                         }
 201
 202                         //name map
 203                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 204                         cdmClass = TaxonNameBase.class;
 205                         idSet = nameIdSet;
 206                         Map<String, Person> nameMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 207                         result.put(nameSpace, nameMap);
 208
 209                         //reference map
 210                         nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
 211                         cdmClass = Reference.class;
 212                         idSet = referenceIdSet;
 213                         Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 214                         result.put(nameSpace, referenceMap);
 215
 216                         //refDetail map
 217                         nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
 218                         cdmClass = Reference.class;
 219                         idSet = refDetailIdSet;
 220                         Map<String, Reference> refDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 221                         result.put(nameSpace, refDetailMap);
 222
 223                 } catch (SQLException e) {
 224                         throw new RuntimeException(e);
 225                 }
 226                 return result;
 227         }
 228
 229         private boolean makeReference(IImportConfigurator config, NomenclaturalStatus nomStatus,
 230                         int nameId, ResultSet rs, ResultSetPartitioner partitioner)
 231                         throws SQLException{
 232
 233                 Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
 234                 Map<String, Reference> refDetailMap = partitioner.getObjectMap(BerlinModelRefDetailImport.REFDETAIL_NAMESPACE);
 235
 236                 Object nomRefFkObj = rs.getObject("NomStatusRefFk");
 237                 Object nomRefDetailFkObj = rs.getObject("NomStatusRefDetailFk");
 238                 //TODO
 239 //              boolean refDetailPrelim = rs.getBoolean("RefDetailPrelim");
 240
 241                 boolean success = true;
 242                 //nomenclatural Reference
 243                 if (refMap != null){
 244                         if (nomRefFkObj != null){
 245                                 String nomRefFk = String.valueOf(nomRefFkObj);
 246                                 String nomRefDetailFk = String.valueOf(nomRefDetailFkObj);
 247                                 Reference<?> ref = getReferenceFromMaps(refDetailMap, refMap, nomRefDetailFk, nomRefFk);
 248
 249                                 //setRef
 250                                 if (ref == null ){
 251                                         //TODO
 252                                         if (! config.isIgnoreNull()){logger.warn("Reference (refFk = " + nomRefFk + ") for NomStatus of TaxonName (nameId = " + nameId + ")"+
 253                                                 " was not found in reference store. Nomenclatural status reference was not set!!");}
 254                                 }else{
 255                                         nomStatus.setCitation(ref);
 256                                 }
 257                         }
 258                 }
 259                 return success;
 260         }
 261
 262         /* (non-Javadoc)
 263          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 264          */
 265         @Override
 266         protected boolean doCheck(BerlinModelImportState state){
 267                 IOValidator<BerlinModelImportState> validator = new BerlinModelNameStatusImportValidator();
 268                 return validator.validate(state);
 269         }
 270
 271
 272         /* (non-Javadoc)
 273          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 274          */
 275         protected boolean isIgnore(BerlinModelImportState state){
 276                 return ! state.getConfig().isDoNameStatus();
 277         }
 278
 279
 280 }