cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/SchemaUpdater_31_33.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.database.update.v31_33;
  12
  13 import java.util.ArrayList;
  14 import java.util.List;
  15
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.database.update.ColumnAdder;
  19 import eu.etaxonomy.cdm.database.update.ColumnRemover;
  20 import eu.etaxonomy.cdm.database.update.ISchemaUpdater;
  21 import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
  22 import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;
  23 import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;
  24 import eu.etaxonomy.cdm.database.update.TableDroper;
  25 import eu.etaxonomy.cdm.database.update.v30_31.SchemaUpdater_30_301;
  26
  27
  28 /**
  29  * NOT YET USED
  30  * @author a.mueller
  31  * @created Oct 11, 2011
  32  */
  33 public class SchemaUpdater_31_33 extends SchemaUpdaterBase {
  34
  35
  36         @SuppressWarnings("unused")
  37         private static final Logger logger = Logger.getLogger(SchemaUpdater_31_33.class);
  38         private static final String startSchemaVersion = "3.0.1.0.201104190000";
  39         private static final String endSchemaVersion = "3.3.0.0.201306010000";
  40
  41 // ********************** FACTORY METHOD *******************************************
  42
  43         public static SchemaUpdater_31_33 NewInstance(){
  44                 return new SchemaUpdater_31_33();
  45         }
  46
  47         /**
  48          * @param startSchemaVersion
  49          * @param endSchemaVersion
  50          */
  51         protected SchemaUpdater_31_33() {
  52                 super(startSchemaVersion, endSchemaVersion);
  53         }
  54
  55         /* (non-Javadoc)
  56          * @see eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getUpdaterList()
  57          */
  58         @Override
  59         protected List<ISchemaUpdaterStep> getUpdaterList() {
  60
  61                 List<ISchemaUpdaterStep> stepList = new ArrayList<ISchemaUpdaterStep>();
  62
  63                 //TODO still needed? Does it throw exception if table does not exist?
  64                 //drop TypeDesignationBase_TaxonNameBase   //from schemaUpdater 301_31
  65                 String stepName = "Drop duplicate TypeDesignation-TaxonName table";
  66                 String tableName = "TypeDesignationBase_TaxonNameBase";
  67                 ISchemaUpdaterStep step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
  68                 stepList.add(step);
  69
  70                 //create original source type column
  71                 stepName = "Create original source type column";
  72                 tableName = "OriginalSourceBase";
  73                 String columnName = "type";
  74                 //TODO NOT NULL unclear
  75                 step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, true, null);
  76                 stepList.add(step);
  77
  78                 //TODO ?? update original source type
  79                 updateOriginalSourceType(stepList);
  80
  81                 //create and update elevenation max, remove error column
  82                 updateElevationMax(stepList);
  83
  84                 //create taxon node tree index
  85                 stepName = "Create taxon node tree index";
  86                 tableName = "TaxonNode";
  87                 columnName = "treeIndex";
  88                 //TODO NOT NULL unclear
  89                 step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
  90                 stepList.add(step);
  91
  92                 //TODO update tree index
  93
  94                 //create original source type column
  95                 stepName = "Create taxon node sort index column";
  96                 tableName = "TaxonNode";
  97                 columnName = "sortIndex";
  98                 step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, null);
  99                 stepList.add(step);
 100
 101                 //TODO implement sorted behaviour in model first !!
 102                 //TODO update sortindex (similar updater exists already for FeatureNode#sortIndex in schema update 25_30
 103
 104                 //create feature node tree index
 105                 stepName = "Create feature node tree index";
 106                 tableName = "FeatureNode";
 107                 columnName = "treeIndex";
 108                 //TODO NOT NULL unclear
 109                 step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
 110                 stepList.add(step);
 111
 112                 //TODO update tree index for feature node
 113
 114                 //update introduced: adventitious (casual) label
 115                 //#3540
 116                 stepName = "Update introduced: adventitious (casual) label";
 117                 String query = " UPDATE representation r " +
 118                                 " SET r.abbreviatedlabel = 'ia' " +
 119                                 " WHERE r.abbreviatedlabel = 'id' AND r.label = 'introduced: adventitious (casual)' ";
 120                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 121                 stepList.add(step);
 122
 123                 //TODO update idInVocabulary for DefinedTerms
 124
 125                 //TODO update termType for DefinedTerms and TermVocabulary, no type must be null
 126
 127                 //TODO update DTYPE for modifiers (Stage, Scope, Sex, DeterminationModifier, Modifier -> DefinedTerm)
 128
 129
 130                 //TODO update rankClass (#3521)
 131
 132                 //TODO change column type for DistanceToWaterSurface und DistanceToGround
 133
 134                 //TODO add column for DistanceToWaterSurfaceMax/Text und DistanceToGroundMax/Text
 135
 136                 //TODO update datatype of sequence.sequence (keeping data not necessary #3325)
 137
 138                 //TODO update datatype->CLOB for URIs. (DefinedTerms, TermVocabulary, Reference
 139                 //Rights, MediaRepresentationPart, GenBankAccession, ) #3345
 140
 141                 //TODO remove table Sequence_GenBankAccession
 142
 143                 //TODO remove table GenBankAccession
 144
 145                 //TODO add columns GenBankAccessionNumber(String) and GenBankUri (URI) to Sequence
 146
 147                 //update Sicilia -> Sicily
 148                 //#3540
 149                 stepName = "Update Sicilia -> Sicily";
 150                 query = " UPDATE representation r " +
 151                                 " SET r.label = 'Sicily', r.text = 'Sicily' " +
 152                                 " WHERE (r.abbreviatedlabel = 'SIC-SI'  OR r.abbreviatedlabel = 'SIC')  AND r.label = 'Sicilia' ";
 153                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 154                 stepList.add(step);
 155
 156                 //remove homotypical group form type designation base
 157                 stepName = "Remove column homotypical group in type designation base";
 158                 tableName = "TypeDesignationBase";
 159                 String oldColumnName = "homotypicalgroup_id";
 160                 step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
 161                 stepList.add(step);
 162
 163                 //add publish flag to taxon
 164                 stepName = "Add publish flag column to taxon base";
 165                 tableName = "TaxonBase";
 166                 columnName = "publish";
 167                 step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, true);
 168                 stepList.add(step);
 169
 170                 //add publish flag to specimen
 171                 stepName = "Add publish flag column to SpecimenOrObservationBase";
 172                 tableName = "SpecimenOrObservationBase";
 173                 columnName = "publish";
 174                 step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, true);
 175                 stepList.add(step);
 176
 177                 //TODO add columns abbrevTitle, abbrevTitleCache and protectedAbbrevTitleCache to Reference
 178
 179
 180                 //add start number to PolytomousKey
 181                 stepName = "Add start number column to PolytomousKey";
 182                 tableName = "PolytomousKey";
 183                 columnName = "startNumber";
 184                 Integer defaultValue = 1;
 185                 step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT,  defaultValue, true);
 186                 stepList.add(step);
 187
 188                 //TODO add specimenOrObservation basis of record to SpecimenOrObservationBase
 189
 190                 //add kindOfUnit to SpecimenOrObservationBase
 191                 stepName = "Add kindOfUnit column to SpecimenOrObservationBase";
 192                 tableName = "SpecimenOrObservationBase";
 193                 columnName = "kindOfUnit";
 194                 String relatedTable = "DefinedTermBase";
 195                 step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT,  true, relatedTable);
 196                 stepList.add(step);
 197
 198
 199                 return stepList;
 200         }
 201
 202         private void updateElevationMax(List<ISchemaUpdaterStep> stepList) {
 203                 //create column
 204                 String stepName = "Create absoluteElevationMax column";
 205                 String tableName = "GatheringEvent";
 206                 String columnName = "absoluteElevationMax";
 207                 ISchemaUpdaterStep step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, null);
 208                 stepList.add(step);
 209
 210
 211                 //update max
 212                 stepName = "Update gathering elevation max";
 213                 //all audits to unknown type
 214                 String query = " UPDATE GatheringEvent ge " +
 215                                 " SET ge.absoluteElevationMax = ge.elevation + ge.elevationErrorRadius,  " +
 216                                 "     ge.absoluteElevation =  ge.elevationErrorRadius - ge.elevationErrorRadius" +
 217                                 " WHERE ge.elevationErrorRadius is not null ";
 218                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 219                 stepList.add(step);
 220                 //TODO same for AUD
 221
 222                 //remove error column
 223                 stepName = "Remove elevationErrorRadius column";
 224                 tableName = "GatheringEvent";
 225                 columnName = "elevationErrorRadius";
 226                 step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
 227                 stepList.add(step);
 228
 229
 230         }
 231
 232         /**
 233          * @param stepList
 234          */
 235         private void updateOriginalSourceType(List<ISchemaUpdaterStep> stepList) {
 236                 String stepName;
 237                 ISchemaUpdaterStep step;
 238                 stepName = "Create original source type column";
 239                 //all audits to unknown type
 240                 String query = "UPDATE OriginalSourceBase_AUD SET type = 0 ";
 241                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 242                 stepList.add(step);
 243
 244                  //all data to unknown
 245                 query = "UPDATE OriginalSourceBase SET type = 0 ";
 246                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 247                 stepList.add(step);
 248
 249                  //all imports recognized by idInSOurce and by missing nameInSource
 250                 query = "UPDATE OriginalSourceBase SET type = 3 WHERE " +
 251                                 "((idInSource IS NOT NULL) OR (idNamespace IS NOT NULL))  AND " +
 252                                 "( nameUsedInSource IS NULL AND originalNameString IS NULL ) ";
 253                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 254                 stepList.add(step);
 255                  //all imports recognized by idInSOurce and by missing nameInSource
 256                 query = "UPDATE OriginalSourceBase SET type = 1 WHERE " +
 257                                 "(idInSource IS NULL AND idNamespace IS NULL) AND " +
 258                                 "( citation IS NOT NULL ) ";
 259                 step = SimpleSchemaUpdaterStep.NewInstance(stepName, query);
 260                 stepList.add(step);
 261         }
 262
 263         /* (non-Javadoc)
 264          * @see eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getNextUpdater()
 265          */
 266         @Override
 267         public ISchemaUpdater getNextUpdater() {
 268                 return null;
 269         }
 270
 271         /* (non-Javadoc)
 272          * @see eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getPreviousUpdater()
 273          */
 274         @Override
 275         public ISchemaUpdater getPreviousUpdater() {
 276                 return SchemaUpdater_30_301.NewInstance();
 277         }
 278
 279 }