cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/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.in;
  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_ALTERNATIVE_NAME_FOR;
  14 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_BASIONYM_FOR;
  15 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_CONSERVED_TYPE_OF;
  16 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FEMALE_PARENT_OF;
  17 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FIRST_PARENT_OF;
  18 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_HOMONYM_OF;
  19 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_VALIDATION_OF;
  20 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LECTOTYPE_OF;
  21 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_MALE_PARENT_OF;
  22 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
  23 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REJECTED_TYPE_OF;
  24 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REPLACED_SYNONYM_FOR;
  25 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_SECOND_PARENT_OF;
  26 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF;
  27 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_VALIDATION_OF;
  28 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_TYPE_NOT_DESIGNATED;
  29 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF;
  30
  31 import java.lang.reflect.Method;
  32 import java.sql.ResultSet;
  33 import java.sql.SQLException;
  34 import java.util.HashMap;
  35 import java.util.HashSet;
  36 import java.util.Map;
  37 import java.util.Set;
  38
  39 import org.apache.commons.lang.StringUtils;
  40 import org.apache.log4j.Logger;
  41 import org.springframework.stereotype.Component;
  42
  43 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  44 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonNameRelationImportValidator;
  45 import eu.etaxonomy.cdm.io.common.IOValidator;
  46 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  47 import eu.etaxonomy.cdm.model.agent.Person;
  48 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  49 import eu.etaxonomy.cdm.model.common.CdmBase;
  50 import eu.etaxonomy.cdm.model.name.BotanicalName;
  51 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  52 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  53 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  54 import eu.etaxonomy.cdm.model.name.NonViralName;
  55 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  56 import eu.etaxonomy.cdm.model.reference.Reference;
  57 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  58
  59 /**
  60  * @author a.mueller
  61  * @created 20.03.2008
  62  * @version 1.0
  63  */
  64 @Component
  65 public class BerlinModelTaxonNameRelationImport extends BerlinModelImportBase {
  66         private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameRelationImport.class);
  67
  68         private static int modCount = 5000;
  69         private static final String pluralString = "name relations";
  70         private static final String dbTableName = "RelName";
  71
  72
  73         public BerlinModelTaxonNameRelationImport(){
  74                 super();
  75         }
  76
  77
  78
  79         @Override
  80         protected String getIdQuery(BerlinModelImportState state) {
  81                 if (StringUtils.isNotBlank(state.getConfig().getNameIdTable())){
  82                         String result = super.getIdQuery(state);
  83                         result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR ";
  84                         result += "       nameFk2 IN (SELECT NameId FROM %s)";
  85                         result = String.format(result, state.getConfig().getNameIdTable(),state.getConfig().getNameIdTable() );
  86                         return result;
  87                 }else{
  88                         return super.getIdQuery(state);
  89                 }
  90         }
  91
  92
  93         /* (non-Javadoc)
  94          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  95          */
  96         @Override
  97         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  98                         String strQuery =
  99                                         " SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
 100                                         " FROM Name as FromName INNER JOIN " +
 101                         " RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
 102                         " Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
 103                         " RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
 104             " WHERE (RelNameId IN ("+ID_LIST_TOKEN +"))";
 105                 return strQuery;
 106         }
 107
 108         /* (non-Javadoc)
 109          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
 110          */
 111         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
 112                 boolean success = true ;
 113                 BerlinModelImportConfigurator config = state.getConfig();
 114                 Set<TaxonNameBase> nameToSave = new HashSet<TaxonNameBase>();
 115                 Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
 116                 Map<String, Reference> biblioRefMap = partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
 117                 Map<String, Reference> nomRefMap = partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);
 118
 119
 120                 ResultSet rs = partitioner.getResultSet();
 121                 try {
 122
 123                         int i = 0;
 124                         //for each name relation
 125                         while (rs.next()){
 126
 127                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelName handled: " + (i-1));}
 128
 129                                 int relNameId = rs.getInt("RelNameId");
 130                                 int name1Id = rs.getInt("name1Id");
 131                                 int name2Id = rs.getInt("name2Id");
 132                                 Object relRefFkObj = rs.getObject("refFk");
 133                                 String details = rs.getString("details");
 134                                 int relQualifierFk = rs.getInt("relNameQualifierFk");
 135                                 String notes = rs.getString("notes");
 136
 137                                 TaxonNameBase<?,?> nameFrom = nameMap.get(String.valueOf(name1Id));
 138                                 TaxonNameBase<?,?> nameTo = nameMap.get(String.valueOf(name2Id));
 139
 140
 141                                 Reference<?> citation = null;
 142                                 if (relRefFkObj != null){
 143                                         String relRefFk = String.valueOf(relRefFkObj);
 144                                         //get nomRef
 145                                         citation = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap,
 146                                                         relRefFk);
 147                                         }
 148
 149                                 //TODO (preliminaryFlag = true testen
 150                                 String microcitation = details;
 151                                 String rule = null;
 152
 153                                 if (nameFrom != null && nameTo != null){
 154                                         success = handleNameRelationship(success, config, name1Id, name2Id,     relQualifierFk,
 155                                                         notes, nameFrom, nameTo, citation, microcitation, rule);
 156
 157                                         if (! nameFrom.isProtectedTitleCache()){
 158                                                 nameFrom.setTitleCache(null);
 159                                                 nameFrom.getTitleCache();
 160                                         }
 161                                         if (! nameTo.isProtectedTitleCache()){
 162                                                 nameTo.setTitleCache(null);
 163                                                 nameTo.getTitleCache();
 164                                         }
 165                                         nameToSave.add(nameFrom);
 166
 167                                         //TODO
 168                                         //ID
 169                                         //etc.
 170                                 }else{
 171                                         //TODO
 172                                         if (nameFrom == null){
 173                                                  logger.warn("from TaxonName " + name1Id + "  for RelName (" + relNameId + " , type: " + relQualifierFk + ") does not exist in store. ToName is: " + (nameTo == null ? "" : nameTo.getTitleCache()));
 174                                         }
 175                                         if (nameTo == null){
 176                                                 logger.warn("to TaxonName " + name2Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + ") does not exist in store. FromName is: "  + (nameFrom == null ? "" : nameFrom.getTitleCache()));
 177                                         }
 178                                         success = false;
 179                                 }
 180                         }
 181
 182
 183                         partitioner.startDoSave();
 184                         getNameService().save(nameToSave);
 185
 186                         return success;
 187                 } catch (SQLException e) {
 188                         logger.error("SQLException:" +  e);
 189                         return false;
 190                 }
 191         }
 192
 193         /**
 194          * @param success
 195          * @param config
 196          * @param name1Id
 197          * @param name2Id
 198          * @param relQualifierFk
 199          * @param notes
 200          * @param nameFrom
 201          * @param nameTo
 202          * @param citation
 203          * @param microcitation
 204          * @param rule
 205          * @return
 206          */
 207         private boolean handleNameRelationship(boolean success,
 208                                 BerlinModelImportConfigurator config, int name1Id, int name2Id,
 209                                 int relQualifierFk, String notes, TaxonNameBase nameFrom,
 210                                 TaxonNameBase nameTo, Reference<?> citation,
 211                                 String microcitation, String rule) {
 212                 AnnotatableEntity nameRelationship = null;
 213                 if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
 214                         nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule);
 215                 }else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
 216                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
 217                 }else if (relQualifierFk == NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF){
 218                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
 219                 }else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
 220                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule) ;
 221                 }else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
 222                         nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());
 223                 }else if (relQualifierFk == NAME_REL_IS_VALIDATION_OF){
 224                         nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.VALIDATED_BY_NAME(), citation, microcitation, rule) ;
 225                 }else if (relQualifierFk == NAME_REL_IS_LATER_VALIDATION_OF){
 226                         nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.LATER_VALIDATED_BY_NAME(), citation, microcitation, rule) ;
 227                 }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 ){
 228                         boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF);
 229                         boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF);
 230                         boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF);
 231                         boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED);
 232
 233                         NameTypeDesignationStatus status = null;
 234                         String originalNameString = null;
 235                         //TODO addToAllNames true or false?
 236                         boolean addToAllNames = false;
 237                         if (config.getNameTypeDesignationStatusMethod() != null){
 238                                 Method method = config.getNameTypeDesignationStatusMethod();
 239                                 method.setAccessible(true);
 240                                 try {
 241                                         status = (NameTypeDesignationStatus)method.invoke(null, notes);
 242                                         nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames);
 243                                 } catch (Exception e) {
 244                                         throw new RuntimeException(e);
 245                                 }
 246                         }else{
 247                                 if (isLectoType){
 248                                         status = NameTypeDesignationStatus.LECTOTYPE();
 249                                 }
 250                                 nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, /*isLectoType,*/ isNotDesignated, addToAllNames);
 251                         }
 252
 253                 }else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
 254                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule) ;
 255                 }else if (relQualifierFk == NAME_REL_IS_ALTERNATIVE_NAME_FOR){
 256                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ALTERNATIVE_NAME(), citation, microcitation, rule) ;
 257                 }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){
 258                         //HybridRelationships
 259                         if (! (nameTo instanceof NonViralName ) || ! (nameFrom instanceof NonViralName)){
 260                                 logger.warn("HybridrelationshipNames ("+name1Id +"," + name2Id +") must be of type NonViralNameName but are not");
 261                                 success = false;
 262                         }
 263                         try {
 264                                 HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk);
 265                                 BotanicalName parent = (BotanicalName)nameFrom;
 266                                 BotanicalName child = (BotanicalName)nameTo;
 267
 268                                 nameRelationship = parent.addHybridChild(child, hybridRelType, rule);
 269
 270                         } catch (UnknownCdmTypeException e) {
 271                                 logger.warn(e);
 272                                 success = false;
 273                         }
 274                 }else {
 275                         //TODO
 276                         Method method = config.getNamerelationshipTypeMethod();
 277                         if (method != null){
 278                                 try {
 279                                         method.invoke(null, relQualifierFk, nameTo, nameFrom);
 280                                 } catch (Exception e) {
 281                                         logger.error(e.getMessage());
 282                                         logger.warn("NameRelationship could not be imported");
 283                                         success = false;
 284                                 }
 285                         }else{
 286                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 287                                 success = false;
 288                         }
 289                 }
 290                 doNotes(nameRelationship, notes);
 291                 return success;
 292         }
 293
 294         /* (non-Javadoc)
 295          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 296          */
 297         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 298                 String nameSpace;
 299                 Class cdmClass;
 300                 Set<String> idSet;
 301                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 302
 303                 try{
 304                         Set<String> nameIdSet = new HashSet<String>();
 305                         Set<String> referenceIdSet = new HashSet<String>();
 306                         Set<String> refDetailIdSet = new HashSet<String>();
 307                         while (rs.next()){
 308                                 handleForeignKey(rs, nameIdSet, "name1Id");
 309                                 handleForeignKey(rs, nameIdSet, "name2Id");
 310                                 handleForeignKey(rs, referenceIdSet, "RefFk");
 311                                 handleForeignKey(rs, refDetailIdSet, "RefDetailFk");
 312         }
 313
 314                         //name map
 315                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 316                         cdmClass = TaxonNameBase.class;
 317                         idSet = nameIdSet;
 318                         Map<String, Person> objectMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 319                         result.put(nameSpace, objectMap);
 320
 321                         //nom reference map
 322                         nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
 323                         cdmClass = Reference.class;
 324                         idSet = referenceIdSet;
 325                         Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 326                         result.put(nameSpace, nomReferenceMap);
 327
 328                         //biblio reference map
 329                         nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
 330                         cdmClass = Reference.class;
 331                         idSet = referenceIdSet;
 332                         Map<String, Reference> biblioReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 333                         result.put(nameSpace, biblioReferenceMap);
 334
 335                         //nom refDetail map
 336                         nameSpace = BerlinModelRefDetailImport.NOM_REFDETAIL_NAMESPACE;
 337                         cdmClass = Reference.class;
 338                         idSet = refDetailIdSet;
 339                         Map<String, Reference> nomRefDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 340                         result.put(nameSpace, nomRefDetailMap);
 341
 342                         //biblio refDetail map
 343                         nameSpace = BerlinModelRefDetailImport.BIBLIO_REFDETAIL_NAMESPACE;
 344                         cdmClass = Reference.class;
 345                         idSet = refDetailIdSet;
 346                         Map<String, Reference> biblioRefDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 347                         result.put(nameSpace, biblioRefDetailMap);
 348
 349                 } catch (SQLException e) {
 350                         throw new RuntimeException(e);
 351                                 }
 352                 return result;
 353         }
 354
 355         /* (non-Javadoc)
 356          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 357          */
 358         @Override
 359         protected boolean doCheck(BerlinModelImportState state){
 360                 IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator();
 361                 return validator.validate(state);
 362         }
 363
 364         /* (non-Javadoc)
 365          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
 366          */
 367         @Override
 368         protected String getTableName() {
 369                 return dbTableName;
 370         }
 371
 372
 373         /* (non-Javadoc)
 374          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
 375          */
 376         @Override
 377         public String getPluralString() {
 378                 return pluralString;
 379                         }
 380
 381         /* (non-Javadoc)
 382          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 383          */
 384         protected boolean isIgnore(BerlinModelImportState state){
 385                 return ! state.getConfig().isDoRelNames();
 386                 }
 387
 388
 389 }