app-import/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_TREATED_AS_LATER_HOMONYM_OF;
  27 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF;
  28 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_VALIDATION_OF;
  29 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_TYPE_NOT_DESIGNATED;
  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.log4j.Logger;
  40 import org.springframework.stereotype.Component;
  41
  42 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  43 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonNameRelationImportValidator;
  44 import eu.etaxonomy.cdm.io.common.IOValidator;
  45 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  46 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  47 import eu.etaxonomy.cdm.model.common.Annotation;
  48 import eu.etaxonomy.cdm.model.common.AnnotationType;
  49 import eu.etaxonomy.cdm.model.common.CdmBase;
  50 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  51 import eu.etaxonomy.cdm.model.name.IBotanicalName;
  52 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  53 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  54 import eu.etaxonomy.cdm.model.name.TaxonName;
  55 import eu.etaxonomy.cdm.model.reference.Reference;
  56 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  57
  58 /**
  59  * @author a.mueller
  60  * @since 20.03.2008
  61  */
  62 @Component
  63 public class BerlinModelTaxonNameRelationImport extends BerlinModelImportBase {
  64
  65     private static final long serialVersionUID = 1197601822023101796L;
  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(dbTableName, pluralString);
  75         }
  76
  77
  78         @Override
  79         protected String getIdQuery(BerlinModelImportState state) {
  80                 String nameIdTable = state.getConfig().getNameIdTable();
  81                 String result = super.getIdQuery(state);
  82             if (isNotBlank(nameIdTable)){
  83                         if (state.getConfig().isEuroMed()){
  84                             result += " WHERE nameFk1 IN (SELECT NameId FROM %s) AND RelNameQualifierFk IN (2, 4, 5, 13, 14, 15, 17, 18, 37, 62) OR ";
  85                             result += "       nameFk2 IN (SELECT NameId FROM %s)  ";
  86                             //the first part is only to check if there are relations that we have maybe missed.
  87                             //2 is unclear, 17 should be in both, 62 links names to itself
  88                             result = String.format(result, nameIdTable, nameIdTable);
  89                         }else{
  90                             result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR ";
  91                             result += "       nameFk2 IN (SELECT NameId FROM %s) ";
  92                             result = String.format(result, nameIdTable, nameIdTable );
  93                         }
  94
  95                 }else{
  96                         //
  97                 }
  98             return result;
  99         }
 100
 101
 102         @Override
 103         protected String getRecordQuery(BerlinModelImportConfigurator config) {
 104                         String strQuery =
 105                                         " SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
 106                                         " FROM Name as FromName INNER JOIN " +
 107                         " RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
 108                         " Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
 109                         " RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
 110             " WHERE (RelNameId IN ("+ID_LIST_TOKEN +"))";
 111                 return strQuery;
 112         }
 113
 114         @Override
 115         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
 116                 boolean success = true ;
 117                 BerlinModelImportConfigurator config = state.getConfig();
 118                 Set<TaxonName> nameToSave = new HashSet<>();
 119                 Map<String, TaxonName> nameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
 120                 Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
 121
 122                 ResultSet rs = partitioner.getResultSet();
 123                 try {
 124
 125                         int i = 0;
 126                         //for each name relation
 127                         while (rs.next()){
 128
 129                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelName handled: " + (i-1));}
 130
 131                                 int relNameId = rs.getInt("RelNameId");
 132                                 int name1Id = rs.getInt("name1Id");
 133                                 int name2Id = rs.getInt("name2Id");
 134                                 Object relRefFkObj = rs.getObject("refFk");
 135                                 String details = rs.getString("details");
 136                                 int relQualifierFk = rs.getInt("relNameQualifierFk");
 137                                 String notes = rs.getString("notes");
 138
 139                                 TaxonName nameFrom = nameMap.get(String.valueOf(name1Id));
 140                                 TaxonName nameTo = nameMap.get(String.valueOf(name2Id));
 141
 142
 143                                 Reference citation = null;
 144                                 if (relRefFkObj != null){
 145                                         String relRefFk = String.valueOf(relRefFkObj);
 146                                         //get nomRef
 147                                         citation = refMap.get(relRefFk);
 148                                 }
 149
 150                                 //TODO (preliminaryFlag = true testen
 151                                 String microcitation = details;
 152                                 String rule = null;
 153
 154                                 if (nameFrom != null && nameTo != null){
 155                                         success = handleNameRelationship(success, config, name1Id, name2Id,     relQualifierFk,
 156                                                         notes, nameFrom, nameTo, citation, microcitation, rule, relNameId);
 157
 158                                         if (! nameFrom.isProtectedTitleCache()){
 159                                                 nameFrom.setTitleCache(null);
 160                                                 nameFrom.getTitleCache();
 161                                         }
 162                                         if (! nameTo.isProtectedTitleCache()){
 163                                                 nameTo.setTitleCache(null);
 164                                                 nameTo.getTitleCache();
 165                                         }
 166                                         nameToSave.add(nameFrom);
 167
 168                                         //TODO
 169                                         //ID
 170                                         //etc.
 171                                 }else{
 172                                         //TODO
 173                                         if (nameFrom == null){
 174                                                 if ( ! (config.isUseEmAreaVocabulary() && relNameId == 28159 )) {
 175                                                         logger.warn("from TaxonName " + name1Id + "  for RelName (" + relNameId + " , type: " + relQualifierFk  + " , toName: " + name2Id+ ") does not exist in store. ToName is: " + (nameTo == null ? "" : nameTo.getTitleCache()));
 176                                                 }
 177                                         }
 178                                         if (nameTo == null){
 179                                                 logger.warn("to TaxonName " + name2Id + " for RelName (" + relNameId + " , type: " + relQualifierFk  + " , fromName: " + name1Id + ") does not exist in store. FromName is: "  + (nameFrom == null ? "" : nameFrom.getTitleCache()));
 180                                         }
 181                                         success = false;
 182                                 }
 183                         }
 184
 185
 186                         partitioner.startDoSave();
 187                         getNameService().save(nameToSave);
 188
 189                         return success;
 190                 } catch (SQLException e) {
 191                         logger.error("SQLException:" +  e);
 192                         return false;
 193                 }
 194         }
 195
 196         /**
 197          * @param success
 198          * @param config
 199          * @param name1Id
 200          * @param name2Id
 201          * @param relQualifierFk
 202          * @param notes
 203          * @param nameFrom
 204          * @param nameTo
 205          * @param citation
 206          * @param microcitation
 207          * @param rule
 208          * @param relNameId
 209          * @return
 210          */
 211         private boolean handleNameRelationship(boolean success,
 212                                 BerlinModelImportConfigurator config, int name1Id, int name2Id,
 213                                 int relQualifierFk, String notes, TaxonName nameFrom,
 214                                 TaxonName nameTo, Reference citation,
 215                                 String microcitation, String rule, int relNameId) {
 216                 AnnotatableEntity nameRelationship = null;
 217                 if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
 218                         nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule, null);
 219                 }else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
 220                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule, null) ;
 221                 }else if (relQualifierFk == NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF){
 222                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule, null) ;
 223                 }else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
 224                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule, null) ;
 225                 }else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
 226                         nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());
 227                 }else if (relQualifierFk == NAME_REL_IS_VALIDATION_OF){
 228                         nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.VALIDATED_BY_NAME(), citation, microcitation, rule, null) ;
 229                 }else if (relQualifierFk == NAME_REL_IS_LATER_VALIDATION_OF){
 230                         nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.LATER_VALIDATED_BY_NAME(), citation, microcitation, rule, null) ;
 231                 }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 ){
 232                         boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF);
 233                         boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF);
 234                         boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF);
 235                         boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED);
 236
 237                         NameTypeDesignationStatus status = null;
 238                         String originalNameString = null;
 239                         //TODO addToAllNames true or false?
 240                         boolean addToAllNames = false;
 241                         if (config.getNameTypeDesignationStatusMethod() != null){
 242                                 Method method = config.getNameTypeDesignationStatusMethod();
 243                                 method.setAccessible(true);
 244                                 try {
 245                                         status = (NameTypeDesignationStatus)method.invoke(null, notes);
 246                                         nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames);
 247                                 } catch (Exception e) {
 248                                         throw new RuntimeException(e);
 249                                 }
 250                         }else{
 251                                 if (isLectoType){
 252                                         status = NameTypeDesignationStatus.LECTOTYPE();
 253                                 }
 254                                 if (isNotDesignated && nameTo == nameFrom){
 255                                     nameFrom = null;  //E+M case
 256                                 }
 257
 258                                 nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, isNotDesignated, addToAllNames);
 259                         }
 260
 261                 }else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
 262                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule, null) ;
 263                 }else if (relQualifierFk == NAME_REL_IS_ALTERNATIVE_NAME_FOR){
 264                         nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ALTERNATIVE_NAME(), citation, microcitation, rule, null) ;
 265                 }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){
 266                         //HybridRelationships
 267                         try {
 268                                 HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk);
 269                                 IBotanicalName parent = nameFrom;
 270                                 IBotanicalName child = nameTo;
 271
 272                                 nameRelationship = parent.addHybridChild(child, hybridRelType, rule);
 273
 274                         } catch (UnknownCdmTypeException e) {
 275                                 logger.warn(e);
 276                                 success = false;
 277                         }
 278                 }else {
 279                         //TODO
 280                         Method method = config.getNamerelationshipTypeMethod();
 281                         if (method != null){
 282                                 try {
 283                                         method.invoke(null, relQualifierFk, nameTo, nameFrom);
 284                                 } catch (Exception e) {
 285                                         logger.error(e.getMessage());
 286                                         logger.warn("NameRelationship could not be imported");
 287                                         success = false;
 288                                 }
 289                         }else{
 290                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 291                                 success = false;
 292                         }
 293                 }
 294                 Annotation annotation = doNotes(nameRelationship, notes);
 295                 if (config.isEuroMed() && annotation != null){
 296                     if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
 297                         annotation.setAnnotationType(AnnotationType.TECHNICAL());
 298                     }else if ((relQualifierFk == NAME_REL_IS_LECTOTYPE_OF) && !notes.contains("designated")){
 299                         annotation.setAnnotationType(AnnotationType.TECHNICAL());
 300                     }else{
 301                         logger.warn("Annotation type not defined for name relationship " + relNameId);
 302                     }
 303                 }else if (annotation != null){
 304             logger.warn("Annotation type not defined for name relationship " + relNameId);
 305                 }
 306                 return success;
 307         }
 308
 309         @Override
 310         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
 311
 312             String nameSpace;
 313                 Set<String> idSet;
 314                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 315
 316                 try{
 317                         Set<String> nameIdSet = new HashSet<>();
 318                         Set<String> referenceIdSet = new HashSet<>();
 319                         Set<String> refDetailIdSet = new HashSet<>();
 320                         while (rs.next()){
 321                                 handleForeignKey(rs, nameIdSet, "name1Id");
 322                                 handleForeignKey(rs, nameIdSet, "name2Id");
 323                                 handleForeignKey(rs, referenceIdSet, "RefFk");
 324                                 handleForeignKey(rs, refDetailIdSet, "RefDetailFk");
 325         }
 326
 327                         //name map
 328                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 329                         idSet = nameIdSet;
 330                         Map<String, TaxonName> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
 331                         result.put(nameSpace, objectMap);
 332
 333                         //reference map
 334                         nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
 335                         idSet = referenceIdSet;
 336                         Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 337                         result.put(nameSpace, referenceMap);
 338
 339                         //refDetail map
 340                         nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
 341                         idSet = refDetailIdSet;
 342                         Map<String, Reference> refDetailMap= getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
 343                         result.put(nameSpace, refDetailMap);
 344
 345                 } catch (SQLException e) {
 346                         throw new RuntimeException(e);
 347                                 }
 348                 return result;
 349         }
 350
 351         @Override
 352         protected boolean doCheck(BerlinModelImportState state){
 353                 IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator();
 354                 return validator.validate(state);
 355         }
 356
 357         @Override
 358     protected boolean isIgnore(BerlinModelImportState state){
 359                 return ! state.getConfig().isDoRelNames();
 360                 }
 361 }