cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v40_41/SchemaUpdater_40_41.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.database.update.v40_41;
  11
  12 import java.util.ArrayList;
  13 import java.util.List;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.common.UTF8;
  18 import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
  19 import eu.etaxonomy.cdm.database.update.ColumnAdder;
  20 import eu.etaxonomy.cdm.database.update.ColumnRemover;
  21 import eu.etaxonomy.cdm.database.update.ISchemaUpdater;
  22 import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
  23 import eu.etaxonomy.cdm.database.update.IndexAdder;
  24 import eu.etaxonomy.cdm.database.update.LanguageStringTableCreator;
  25 import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;
  26 import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;
  27 import eu.etaxonomy.cdm.database.update.SortIndexUpdater;
  28 import eu.etaxonomy.cdm.database.update.TableDroper;
  29 import eu.etaxonomy.cdm.database.update.v36_40.SchemaUpdater_36_40;
  30 import eu.etaxonomy.cdm.database.update.v41_47.SchemaUpdater_41_47;
  31
  32 /**
  33  * @author a.mueller
  34  * @created 16.04.2016
  35  */
  36 public class SchemaUpdater_40_41 extends SchemaUpdaterBase {
  37
  38         @SuppressWarnings("unused")
  39         private static final Logger logger = Logger.getLogger(SchemaUpdater_40_41.class);
  40         private static final String endSchemaVersion = "4.1.0.0.201607300000";
  41         private static final String startSchemaVersion = "4.0.0.0.201604200000";
  42
  43         // ********************** FACTORY METHOD *************************************
  44
  45         public static SchemaUpdater_40_41 NewInstance() {
  46                 return new SchemaUpdater_40_41();
  47         }
  48
  49         /**
  50          * @param startSchemaVersion
  51          * @param endSchemaVersion
  52          */
  53         protected SchemaUpdater_40_41() {
  54                 super(startSchemaVersion, endSchemaVersion);
  55         }
  56
  57         @Override
  58         protected List<ISchemaUpdaterStep> getUpdaterList() {
  59
  60                 String stepName;
  61                 String tableName;
  62                 ISchemaUpdaterStep step;
  63                 String query;
  64                 String newColumnName;
  65                 String oldColumnName;
  66
  67                 List<ISchemaUpdaterStep> stepList = new ArrayList<ISchemaUpdaterStep>();
  68
  69
  70         //#3658 update nomenclatural code
  71         NomenclaturalCodeUpdater.NewInstance(stepList);
  72
  73         //#5970
  74         //Implement allowOverride in CdmPreference
  75         stepName = "Add allowOverride in CdmPreference";
  76         tableName = "CdmPreference";
  77         newColumnName = "allowOverride";
  78         step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, ! INCLUDE_AUDIT, false);
  79         stepList.add(step);
  80
  81         //#5875
  82         //Implement isDefault to DescriptionBase
  83         stepName = "Add isDefault in DescriptionBase";
  84         tableName = "DescriptionBase";
  85         newColumnName = "isDefault";
  86         step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, false);
  87         stepList.add(step);
  88
  89         //#5826
  90         //Cleanup empty name descriptions
  91         stepName = "Cleanup empty name descriptions";
  92 //        query = " DELETE FROM @@DescriptionBase@@ db " +
  93 //                 " WHERE db.DTYPE = 'TaxonNameDescription' " +
  94 //                 " AND NOT EXISTS (SELECT * FROM @@DescriptionElementBase@@ deb WHERE deb.indescription_id = db.id )";
  95         query = "DELETE FROM @@DescriptionBase@@ "
  96                 + " WHERE DTYPE = 'TaxonNameDescription' AND id IN (SELECT id FROM " +
  97                   " (SELECT id FROM DescriptionBase db "
  98                   + "   WHERE NOT EXISTS (SELECT * FROM DescriptionElementBase deb WHERE deb.indescription_id = db.id )"
  99                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_Annotation MN WHERE MN.descriptionbase_id = db.id) "
 100                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_Credit MN WHERE MN.descriptionbase_id = db.id) "
 101                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_Extension MN WHERE MN.descriptionbase_id = db.id) "
 102                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_Identifier MN WHERE MN.descriptionbase_id = db.id) "
 103                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_Marker MN WHERE MN.descriptionbase_id = db.id) "
 104                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_OriginalSourceBase MN WHERE MN.descriptionbase_id = db.id) "
 105                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_Reference MN WHERE MN.descriptionbase_id = db.id) "
 106                   + "   AND NOT EXISTS (SELECT * FROM DescriptionBase_RightsInfo MN WHERE MN.descriptionbase_id = db.id) "
 107                   + "   AND NOT EXISTS (SELECT * FROM WorkingSet_DescriptionBase MN WHERE MN.descriptions_id = db.id) "
 108                   + " ) as drvTbl) ";
 109         SimpleSchemaUpdaterStep simpleStep = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);
 110         stepList.add(simpleStep);
 111
 112         //#5921
 113         //UPDATE congruent symbol in DefinedTermBase
 114         stepName = "UPDATE congruent symbol in DefinedTermBase";
 115         query = " UPDATE @@DefinedTermBase@@ "
 116                 + " SET idInVocabulary = Replace(idInVocabulary, '\u2245', '\u225c'), symbol = Replace(symbol, '\u2245', '\u225c'), inverseSymbol = Replace(inverseSymbol, '\u2245', '\u225c')"
 117                 + " WHERE DTYPE like 'TaxonRel%' "
 118                 + "     AND (idInVocabulary like '%\u2245%' OR symbol like '%\u2245%' OR inverseSymbol like '%\u2245%' )";
 119         simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "DefinedTermBase", -99);
 120         stepList.add(simpleStep);
 121
 122         //#5921
 123         //UPDATE congruent symbol in Representations
 124         stepName = "UPDATE congruent symbol in Representations";
 125         query = " UPDATE @@Representation@@ "
 126                 + " SET abbreviatedLabel = Replace(abbreviatedLabel, '\u2245', '\u225c') "
 127                 + " WHERE (abbreviatedLabel like '%\u2245%' )";
 128         simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "Representation", -99);
 129         stepList.add(simpleStep);
 130
 131
 132         //#5976
 133         //update sortindex on FeatureNode children
 134         stepName = "Update sort index on FeatureNode children";
 135         tableName = "FeatureNode";
 136         String parentIdColumn = "parent_id";
 137         String sortIndexColumn = "sortIndex";
 138         SortIndexUpdater updateSortIndex = SortIndexUpdater.NewUpdateExistingSortindexInstance(stepName, tableName, parentIdColumn, sortIndexColumn, INCLUDE_AUDIT);
 139         stepList.add(updateSortIndex);
 140
 141         //#5976
 142         // update sortindex for TaxonNodes
 143         stepName = "Update sort index on TaxonNode children";
 144         tableName = "TaxonNode";
 145         parentIdColumn = "parent_id";
 146         sortIndexColumn = "sortIndex";
 147         updateSortIndex = SortIndexUpdater.NewUpdateExistingSortindexInstance(
 148                 stepName, tableName, parentIdColumn, sortIndexColumn,
 149                 INCLUDE_AUDIT);
 150         stepList.add(updateSortIndex);
 151
 152         //#5976
 153         stepName = "Update sort index on PolytomousKeyNode children";
 154         tableName = "PolytomousKeyNode";
 155         parentIdColumn = "parent_id";
 156         sortIndexColumn = "sortIndex";
 157         updateSortIndex = SortIndexUpdater.NewUpdateExistingSortindexInstance(
 158                 stepName, tableName, parentIdColumn, sortIndexColumn,
 159                 INCLUDE_AUDIT);
 160         stepList.add(updateSortIndex);
 161
 162         //#3925
 163         //excluded to TaxonNode
 164         stepName = "Add excluded to TaxonNode";
 165         tableName = "TaxonNode";
 166         newColumnName = "excluded";
 167         step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, false);
 168         stepList.add(step);
 169
 170         //#3925
 171         //Move excluded from Taxon to TaxonNode
 172         stepName = "Move excluded from Taxon to TaxonNode";
 173         query = "UPDATE @@TaxonNode@@ tn " +
 174                 " SET excluded = (SELECT DISTINCT excluded FROM @@TaxonBase@@ tb WHERE tb.id = tn.taxon_id)";
 175         simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNode", -99)
 176                 //.addDefaultAuditing("TaxonBase") removed due to non unique results in subquery, solving this problem is too much work to be implemented here, so audited values will not be correct partly but always representing the current state
 177                 ;
 178         stepList.add(simpleStep);
 179
 180         stepName = "Move excluded from Taxon to TaxonNode/set null to false";
 181         query = "UPDATE @@TaxonNode@@ SET excluded = 0 WHERE excluded IS NULL";
 182         simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNode", -99);
 183         simpleStep.put(DatabaseTypeEnum.PostgreSQL, query.replace("0", "false"));
 184         simpleStep.putAudited(DatabaseTypeEnum.PostgreSQL, query.replace("TaxonNode","TaxonNode_AUD").replace("0", "false"));
 185         stepList.add(simpleStep);
 186
 187         //#3925
 188         //remove excluded from TaxonNode
 189         stepName = "Remove excluded from TaxonBase";
 190         tableName = "TaxonBase";
 191         oldColumnName = "excluded";
 192         step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
 193         stepList.add(step);
 194
 195         //#3925
 196         //unplaced to TaxonNode
 197         stepName = "Add unplaced to TaxonNode";
 198         tableName = "TaxonNode";
 199         newColumnName = "unplaced";
 200         step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, false);
 201         stepList.add(step);
 202
 203
 204         //#3925
 205         //Move unplaced from Taxon to TaxonNode
 206
 207         stepName = "Move unplaced from Taxon to TaxonNode";
 208         query = "UPDATE @@TaxonNode@@ tn " +
 209                 " SET unplaced = (SELECT DISTINCT unplaced FROM @@TaxonBase@@ tb WHERE tb.id = tn.taxon_id)";
 210         simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNode", -99)
 211                 //.addDefaultAuditing("TaxonBase") removed due to non unique results in subquery, solving this problem is too much work to be implemented here, so audited values will not be correct partly but always representing the current state
 212                 ;
 213         stepList.add(simpleStep);
 214
 215         stepName = "Move unplaced from Taxon to TaxonNode/set null to false";
 216         query = "UPDATE @@TaxonNode@@ SET unplaced = 0 WHERE unplaced IS NULL";
 217         simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNode", -99);
 218         simpleStep.put(DatabaseTypeEnum.PostgreSQL, query.replace("0", "false"));
 219         simpleStep.putAudited(DatabaseTypeEnum.PostgreSQL, query.replace("TaxonNode","TaxonNode_AUD").replace("0", "false"));
 220         stepList.add(simpleStep);
 221
 222         //#3925
 223         //remove unplaced from TaxonNode
 224         stepName = "Remove unplaced from TaxonBase";
 225         tableName = "TaxonBase";
 226         oldColumnName = "unplaced";
 227         step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
 228         stepList.add(step);
 229
 230         //#5778
 231         //update PresenceAbsenceTerm symbols
 232         updatePresenceAbsenceTermSymbols(stepList);
 233
 234         //#6089
 235         //Remove taxonomicParentCache from Taxon
 236         stepName = "Remove taxonomicParentCache from Taxon";
 237         tableName = "TaxonBase";
 238         oldColumnName = "taxonomicParentCache_id";
 239         step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
 240         stepList.add(step);
 241
 242         //#6089
 243         //Remove taxonomicChildrenCount from Taxon
 244         stepName = "Remove taxonomicChildrenCount from Taxon";
 245         tableName = "TaxonBase";
 246         oldColumnName = "taxonomicChildrenCount";
 247         step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
 248         stepList.add(step);
 249
 250         //#5974 Remove synonym relationships
 251         removeSynonymRelationships_5974(stepList);
 252
 253
 254         //#5981 Add abbreviation to Rank "Cultivar"
 255         stepName = "Add abbreviation to Rank 'Cultivar'";
 256         String updateSql = "UPDATE Representation SET abbreviatedLabel='cv.' WHERE label='Cultivar'";
 257         String nonAuditedTableName = "Representation";
 258         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, nonAuditedTableName, -99);
 259         stepList.add(step);
 260
 261         //#5981  Add abbreviation to idInVoc for 'Cultivar'
 262         stepName = "#5981 Add abbreviation to idInVoc for 'Cultivar'";
 263         updateSql = "UPDATE DefinedTermBase SET idInVocabulary='cv.' WHERE uuid='5e98415b-dc6e-440b-95d6-ea33dbb39ad0'";
 264         nonAuditedTableName = "DefinedTermBase";
 265         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, nonAuditedTableName, -99);
 266         stepList.add(step);
 267
 268         //#5952 Add identityCache
 269         stepName = "Add identityCache";
 270         tableName = "SpecimenOrObservationBase";
 271         newColumnName = "identityCache";
 272         step = ColumnAdder.NewStringInstance (stepName, tableName, newColumnName, INCLUDE_AUDIT);
 273         stepList.add(step);
 274
 275         //index
 276         stepName = "Add identityCache index";
 277         tableName = "SpecimenOrObservationBase";
 278         newColumnName = "identityCache";
 279         step = IndexAdder.NewInstance(stepName, tableName, newColumnName, null);
 280         stepList.add(step);
 281
 282         stepName = "Add protectedIdentityCache";
 283         tableName = "SpecimenOrObservationBase";
 284         newColumnName = "protectedIdentityCache";
 285         step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, false);
 286         stepList.add(step);
 287
 288         //#5634 Add excluded note
 289         stepName = "Add excluded note";
 290         tableName = "TaxonNode";
 291         String attributeName = "excludedNote";
 292         step = LanguageStringTableCreator.NewLanguageStringInstance(stepName, tableName, attributeName, INCLUDE_AUDIT);
 293         stepList.add(step);
 294
 295         return stepList;
 296     }
 297
 298         private void removeSynonymRelationships_5974(List<ISchemaUpdaterStep> stepList) {
 299             //add partial column to Synonym
 300         String stepName = "Add partial column to Synonym";
 301         String tableName = "TaxonBase";
 302         String newColumnName = "partial";
 303         ISchemaUpdaterStep step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, false);
 304         stepList.add(step);
 305
 306             //add proParte column to Synonym
 307         stepName = "Add proParte column to Synonym";
 308         tableName = "TaxonBase";
 309         newColumnName = "proParte";
 310         step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, false);
 311         stepList.add(step);
 312
 313             //add type column to Synonym
 314         stepName = "Add type column to Synonym";
 315         tableName = "TaxonBase";
 316         newColumnName = "type_id";
 317         String referencedTable = "DefinedTermBase";
 318         step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
 319         stepList.add(step);
 320
 321             //add acceptedTaxon_id to Synonym
 322         stepName = "Add acceptedTaxon to Synonym";
 323         tableName = "TaxonBase";
 324         newColumnName = "acceptedTaxon_id";
 325         referencedTable = "TaxonBase";
 326         step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
 327         stepList.add(step);
 328
 329             //move data
 330         //move duplicates first
 331             step = SynonymDeduplicator.NewInstance();
 332         stepList.add(step);
 333
 334         //update pro parte
 335         stepName = "Update proParte";
 336         String updateSql = "UPDATE @@TaxonBase@@ syn " +
 337                 " SET proParte = (SELECT DISTINCT proParte FROM @@SynonymRelationship@@ sr WHERE sr.relatedFrom_id = syn.id) " +
 338                 " WHERE acceptedTaxon_id IS NULL ";
 339         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, "TaxonBase", -99)
 340                 //.addDefaultAuditing("SynonymRelationship")  //difficult to implement due to non-uniqueness in subquery
 341                 ;
 342         stepList.add(step);
 343
 344         updateSql = "UPDATE @@TaxonBase@@ " +
 345                 " SET proParte = @FALSE@ " +
 346                 " WHERE DTYPE='Synonym' AND proParte IS NULL ";
 347         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, "TaxonBase", -99);
 348         stepList.add(step);
 349
 350
 351         //update partial
 352         stepName = "Update partial";
 353         updateSql = "UPDATE @@TaxonBase@@ syn " +
 354                 " SET partial=(SELECT DISTINCT partial FROM @@SynonymRelationship@@ sr WHERE sr.relatedFrom_id = syn.id) " +
 355                 " WHERE acceptedTaxon_id IS NULL ";
 356         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, "TaxonBase", -99)
 357                 //.addDefaultAuditing("SynonymRelationship")  //difficult to implement due to non-uniqueness in subquery
 358                 ;
 359         stepList.add(step);
 360
 361         updateSql = "UPDATE @@TaxonBase@@ " +
 362                 " SET partial = @FALSE@ " +
 363                 " WHERE DTYPE='Synonym' AND partial IS NULL ";
 364         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, "TaxonBase", -99);
 365         stepList.add(step);
 366
 367         //update synonym type
 368         stepName = "Update Synonym type";
 369         updateSql = "UPDATE @@TaxonBase@@ syn " +
 370                 " SET type_id=(SELECT DISTINCT type_id FROM @@SynonymRelationship@@ sr WHERE sr.relatedFrom_id = syn.id)" +
 371                 " WHERE acceptedTaxon_id IS NULL ";
 372         //        String updateSqlAud = updateSql.replace("TaxonBase", "TaxonBase_AUD").replace("SynonymRelationship", "SynonymRelationship_AUD");
 373         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, "TaxonBase", -99);
 374         stepList.add(step);
 375
 376         //update acceptedTaxon_id
 377         stepName = "Update acceptedTaxon_id";
 378         updateSql = "UPDATE @@TaxonBase@@ syn " +
 379                 " SET acceptedTaxon_id=(SELECT DISTINCT relatedTo_id FROM @@SynonymRelationship@@ sr WHERE sr.relatedFrom_id = syn.id)" +
 380                 " WHERE acceptedTaxon_id IS NULL ";
 381 //        updateSqlAud = updateSql.replace("TaxonBase", "TaxonBase_AUD").replace("SynonymRelationship", "SynonymRelationship_AUD");
 382         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, "TaxonBase", -99);
 383         stepList.add(step);
 384
 385
 386
 387             //rename SynonymRelationshipType to SynonymType in DefinedTermBase.DTYPE
 388         stepName = "Rename SynonymRelationshipType to SynonymType in DefinedTermBase.DTYPE";
 389         updateSql = "UPDATE DefinedTermBase SET DTYPE='SynonymType' WHERE DTYPE='SynonymRelationshipType'";
 390         String nonAuditedTableName = "DefinedTermBase";
 391         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, nonAuditedTableName, -99);
 392         stepList.add(step);
 393
 394         //rename SynonymRelationshipType to SynonymType in DefinedTermBase.titleCache
 395         stepName = "Rename SynonymRelationshipType to SynonymType in DefinedTermBase.titleCache";
 396         updateSql = "UPDATE DefinedTermBase SET titleCache='SynonymType' WHERE titleCache='SynonymRelationshipType'";
 397         nonAuditedTableName = "DefinedTermBase";
 398         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, nonAuditedTableName, -99);
 399         stepList.add(step);
 400
 401         //rename SynonymRelationshipType to SynonymType in Representation labels
 402         stepName = "Rename SynonymRelationshipType to SynonymType in Representation labels";
 403         updateSql = "UPDATE Representation SET label='Synonym Type' WHERE label='Synonym Relationship Type'";
 404         nonAuditedTableName = "Representation";
 405         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, nonAuditedTableName, -99);
 406         stepList.add(step);
 407
 408         //rename SynonymRelationshipType to SynonymType in Representation text
 409         stepName = "Rename SynonymRelationshipType to SynonymType in Representation text";
 410         updateSql = "UPDATE Representation SET text='Synonym Type' WHERE text='Synonym Relationship Type'";
 411         nonAuditedTableName = "Representation";
 412         step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, updateSql, nonAuditedTableName, -99);
 413         stepList.add(step);
 414
 415             //remove SynonymRelationship_Annotation
 416         stepName = "Remove SynonymRelationship_Annotation table";
 417         tableName = "SynonymRelationship_Annotation";
 418         step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
 419         stepList.add(step);
 420
 421         //remove SynonymRelationship_Marker
 422         stepName = "Remove SynonymRelationship_Marker table";
 423         tableName = "SynonymRelationship_Marker";
 424         step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
 425         stepList.add(step);
 426
 427         //remove SynonymRelationship table
 428         stepName = "Remove synonym relationship table";
 429         tableName = "SynonymRelationship";
 430         step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
 431         stepList.add(step);
 432         }
 433
 434     /**
 435      * @param stepList
 436      */
 437     private void updatePresenceAbsenceTermSymbols(List<ISchemaUpdaterStep> stepList) {
 438         String enDash = UTF8.EN_DASH.toString();
 439
 440         //endemic
 441         updateSinglePATsymbol(stepList, "c3ee7048-15b7-4be1-b687-9ce9c1a669d6", "e", "" + UTF8.BLACK_CIRCLE);
 442         //present
 443         updateSinglePATsymbol(stepList, "cef81d25-501c-48d8-bbea-542ec50de2c2", "p", "");
 444         //doubtfully present
 445         updateSinglePATsymbol(stepList, "75a60279-a4c2-4f53-bc57-466028a4b3db", "pd", "?");
 446         //native
 447         updateSinglePATsymbol(stepList, "ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7", "n", "");
 448         //native: doubtfully native
 449         updateSinglePATsymbol(stepList, "310373bf-7df4-4d02-8cb3-bcc7448805fc", "nd", "d");
 450         //introduced: naturalized
 451         updateSinglePATsymbol(stepList, "e191e89a-a751-4b0c-b883-7f1de70915c9", "in", "n");
 452         //introduced: adventitious (casual)
 453         updateSinglePATsymbol(stepList, "42946bd6-9c22-45ad-a910-7427e8f60bfd", "ia", "a");
 454         //naturalised
 455         updateSinglePATsymbol(stepList, "4e04990a-66fe-4fdf-856c-f40772fbcf0a", "na", "n");
 456         //native: presence questionable
 457         updateSinglePATsymbol(stepList, "925662c1-bb10-459a-8c53-da5a738ac770", "nq", "?");
 458         //introduced: presence questionable
 459         updateSinglePATsymbol(stepList, "83eb0aa0-1a45-495a-a3ca-bf6958b74366", "iq", "?");
 460         //introduced: cultivated
 461         updateSinglePATsymbol(stepList, "fac8c347-8262-44a1-b0a4-db4de451c021", "ic", "c");
 462         //cultivated, presence questionable
 463         updateSinglePATsymbol(stepList, "4f31bfc8-3058-4d83-aea5-3a1fe9773f9f", "cq", "?c");
 464         //absent
 465         updateSinglePATsymbol(stepList, "59709861-f7d9-41f9-bb21-92559cedd598", "a", enDash);
 466         //reported in error
 467         updateSinglePATsymbol(stepList, "38604788-cf05-4607-b155-86db456f7680", "f", enDash);
 468         //native: reported in error
 469         updateSinglePATsymbol(stepList, "aeec2947-2700-4623-8e32-9e3a430569d1", "if", enDash);
 470         //cultivated: reported in error
 471         updateSinglePATsymbol(stepList, "9d4d3431-177a-4abe-8e4b-1558573169d6", "cf", enDash);
 472
 473     }
 474
 475     /**
 476      * @param uuid the uuid
 477      * @param oldSymbol
 478      * @param newSybol
 479      */
 480     private void updateSinglePATsymbol(List<ISchemaUpdaterStep> stepList,
 481             String uuid, String oldSymbol, String newSymbol) {
 482         String stepName = "Update single symbol for PresenceAbsenceTerm " + uuid;
 483         String query = "UPDATE @@DefinedTermBase@@ dtb "
 484                 + " SET symbol = '" + newSymbol + "'"
 485                 + " WHERE uuid = '" + uuid + "' AND symbol = '" + oldSymbol + "'" ;
 486         SimpleSchemaUpdaterStep simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "DefinedTermBase", -99);
 487         stepList.add(simpleStep);
 488     }
 489
 490     @Override
 491         public ISchemaUpdater getNextUpdater() {
 492                 return SchemaUpdater_41_47.NewInstance();
 493         }
 494
 495         @Override
 496         public ISchemaUpdater getPreviousUpdater() {
 497                 return SchemaUpdater_36_40.NewInstance();
 498         }
 499
 500 }