// $Id$
/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
+ * Copyright (C) 2007 EDIT
+ * European Distributed Institute of Taxonomy
+ * http://www.e-taxonomy.eu
+ *
+ * The contents of this file are subject to the Mozilla Public License Version 1.1
+ * See LICENSE.TXT at the top of this package for the full license terms.
+ */
package eu.etaxonomy.cdm.database.update.v31_33;
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
-
/**
* @author a.mueller
* @created Jun 06, 2013
*/
public class SchemaUpdater_31_33 extends SchemaUpdaterBase {
- private static final Logger logger = Logger.getLogger(SchemaUpdater_31_33.class);
+ private static final Logger logger = Logger
+ .getLogger(SchemaUpdater_31_33.class);
private static final String startSchemaVersion = "3.0.1.0.201104190000";
private static final String endSchemaVersion = "3.3.0.0.201309240000";
-
-// ********************** FACTORY METHOD *******************************************
-
- public static SchemaUpdater_31_33 NewInstance(){
+
+ // ********************** FACTORY METHOD
+ // *******************************************
+
+ public static SchemaUpdater_31_33 NewInstance() {
return new SchemaUpdater_31_33();
}
-
+
/**
* @param startSchemaVersion
* @param endSchemaVersion
protected SchemaUpdater_31_33() {
super(startSchemaVersion, endSchemaVersion);
}
-
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getUpdaterList()
*/
@Override
protected List<ISchemaUpdaterStep> getUpdaterList() {
-
+
String stepName;
String tableName;
ISchemaUpdaterStep step;
String columnName;
-
- //CHECKS
-
- //remove SpecimenOrObservationBase_Media #3597
- //TODO check if Description -Specimen Relation has M:M data
- if (false){
- throw new RuntimeException("Required check for SpecimenOrObservationBase_Media");
- }else{
+
+ // CHECKS
+
+ // remove SpecimenOrObservationBase_Media #3597
+ // TODO check if Description -Specimen Relation has M:M data
+ if (false) {
+ throw new RuntimeException(
+ "Required check for SpecimenOrObservationBase_Media");
+ } else {
logger.warn("CHECKS for inconsistent data not running !!!!");
}
-
-
+
List<ISchemaUpdaterStep> stepList = new ArrayList<ISchemaUpdaterStep>();
-
- //Was in Schemaupdater_301_31 which was never used and later deleted (r18331).
- //drop TypeDesignationBase_TaxonNameBase //from schemaUpdater 301_31
+
+ // Was in Schemaupdater_301_31 which was never used and later deleted
+ // (r18331).
+ // drop TypeDesignationBase_TaxonNameBase //from schemaUpdater 301_31
stepName = "Drop duplicate TypeDesignation-TaxonName table";
tableName = "TypeDesignationBase_TaxonNameBase";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
-
- //create original source type column
+
+ // create original source type column
stepName = "Create original source type column";
tableName = "OriginalSourceBase";
columnName = "sourceType";
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 4, INCLUDE_AUDIT);
- ((ColumnAdder)step).setNotNull(true);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 4, INCLUDE_AUDIT);
+ ((ColumnAdder) step).setNotNull(true);
stepList.add(step);
-
- //update original source type
+
+ // update original source type
updateOriginalSourceType(stepList);
-
- //create and update elevenation max, remove error column
+
+ // create and update elevenation max, remove error column
updateElevationMax(stepList);
-
- //create TaxonNode tree index
+
+ // create TaxonNode tree index
stepName = "Create taxon node tree index";
tableName = "TaxonNode";
columnName = "treeIndex";
- //TODO NOT NULL unclear //see also columnTypeChanger
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ // TODO NOT NULL unclear //see also columnTypeChanger
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 255, INCLUDE_AUDIT);
stepList.add(step);
-
- //update treeindex for taxon nodes
+
+ // update treeindex for taxon nodes
stepName = "Update TaxonNode treeindex";
tableName = "TaxonNode";
String treeIdColumnName = "classification_id";
- step = TreeIndexUpdater.NewInstance(stepName, tableName, treeIdColumnName, columnName, INCLUDE_AUDIT);
+ step = TreeIndexUpdater.NewInstance(stepName, tableName,
+ treeIdColumnName, columnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //create TaxonNode sort index column
+
+ // create TaxonNode sort index column
stepName = "Create taxon node sort index column";
tableName = "TaxonNode";
columnName = "sortIndex";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, null);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false, null);
stepList.add(step);
-
- //TODO implement sorted behaviour in model first !!
- //update sortindex
+
+ // TODO implement sorted behaviour in model first !!
+ // update sortindex
stepName = "Update sort index on TaxonNode children";
tableName = "TaxonNode";
String parentIdColumn = "parent_id";
String sortIndexColumn = "sortIndex";
- SortIndexUpdater updateSortIndex = SortIndexUpdater.NewInstance(stepName, tableName, parentIdColumn, sortIndexColumn, INCLUDE_AUDIT);
+ SortIndexUpdater updateSortIndex = SortIndexUpdater.NewInstance(
+ stepName, tableName, parentIdColumn, sortIndexColumn,
+ INCLUDE_AUDIT);
stepList.add(updateSortIndex);
- //Classification root nodes sort index
+ // Classification root nodes sort index
stepName = "Create classification root node sort index column";
tableName = "Classification_TaxonNode";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, null);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false, null);
stepList.add(step);
stepName = "Update sort index on classification child nodes";
parentIdColumn = "Classification_id";
String idColumn = "rootnodes_id";
- updateSortIndex = SortIndexUpdater.NewInstance(stepName, tableName, parentIdColumn, sortIndexColumn, idColumn, INCLUDE_AUDIT);
+ updateSortIndex = SortIndexUpdater.NewInstance(stepName, tableName,
+ parentIdColumn, sortIndexColumn, idColumn, INCLUDE_AUDIT);
stepList.add(updateSortIndex);
-
- //create feature node tree index
+ // create feature node tree index
stepName = "Create feature node tree index";
tableName = "FeatureNode";
columnName = "treeIndex";
- //TODO NOT NULL unclear
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ // TODO NOT NULL unclear
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 255, INCLUDE_AUDIT);
stepList.add(step);
-
- //update tree index for feature node
+
+ // update tree index for feature node
stepName = "Update FeatureNode treeindex";
tableName = "FeatureNode";
treeIdColumnName = "featuretree_id";
- step = TreeIndexUpdater.NewInstance(stepName, tableName, treeIdColumnName, columnName, INCLUDE_AUDIT);
+ step = TreeIndexUpdater.NewInstance(stepName, tableName,
+ treeIdColumnName, columnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //update introduced: adventitious (casual) label
- //#3540
+
+ // update introduced: adventitious (casual) label
+ // #3540
stepName = "Update introduced: adventitious (casual) label";
- String query = " UPDATE Representation r " +
- " SET r.abbreviatedlabel = 'ia' " +
- " WHERE r.abbreviatedlabel = 'id' AND r.label = 'introduced: adventitious (casual)' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing("Representation");
+ String query = " UPDATE Representation r "
+ + " SET r.abbreviatedlabel = 'ia' "
+ + " WHERE r.abbreviatedlabel = 'id' AND r.label = 'introduced: adventitious (casual)' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing("Representation");
stepList.add(step);
-
- //termType for DefinedTerms and TermVocabulary, no type must be null
+
+ // termType for DefinedTerms and TermVocabulary, no type must be null
stepName = "Create termType column in DefinedTermBase";
tableName = "DefinedTermBase";
columnName = "termType";
- //TODO NOT NULL unclear
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ // TODO NOT NULL unclear
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 255, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Create termType column in TermVocabulary";
tableName = "TermVocabulary";
columnName = "termType";
- //TODO NOT NULL unclear
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 4, INCLUDE_AUDIT);
+ // TODO NOT NULL unclear
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 4, INCLUDE_AUDIT);
stepList.add(step);
-
-
- //update termType for DefinedTerms, no type must be null
+
+ // update termType for DefinedTerms, no type must be null
updateTermTypesForTerms(stepList);
-
- //update termType for TermVocabulary, no type must be null
+
+ // update termType for TermVocabulary, no type must be null
updateTermTypesForVocabularies(stepList);
- //update DTYPE of DefinedTerms
+ // update DTYPE of DefinedTerms
updateDtypeOfDefinedTerms(stepList);
- //idInVocabulary for DefinedTerms
+ // idInVocabulary for DefinedTerms
stepName = "Create idInVocabulary column in DefinedTermBase";
tableName = "DefinedTermBase";
columnName = "idInVocabulary";
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 255, INCLUDE_AUDIT);
stepList.add(step);
-
- //update idInVocabulary
+
+ // update idInVocabulary
updateIdInVocabulary(stepList);
-
- //rankClass (#3521)
+
+ // rankClass (#3521)
stepName = "Create rankClass column in DefinedTermBase";
tableName = "DefinedTermBase";
columnName = "rankClass";
- //TODO NOT NULL unclear
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ // TODO NOT NULL unclear
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ 255, INCLUDE_AUDIT);
stepList.add(step);
-
- //update rankClass (#3521)
+
+ // update rankClass (#3521)
step = RankClassUpdater.NewInstance();
stepList.add(step);
-
- //update datatype->CLOB for URIs. (DefinedTerms, TermVocabulary, Reference, Rights, MediaRepresentationPart )
- //#3345, TODO adapt type to <65k
- //TODO sequence.sequence has been changed #3360
+
+ // update datatype->CLOB for URIs. (DefinedTerms, TermVocabulary,
+ // Reference, Rights, MediaRepresentationPart )
+ // #3345, TODO adapt type to <65k
+ // TODO sequence.sequence has been changed #3360
changeUriType(stepList);
-
- //Annotation.linkbackUri change name #3374
+
+ // Annotation.linkbackUri change name #3374
stepName = "Update url to uri (->clob) for Annotation.linkbackUri";
columnName = "linkbackUrl";
String newColumnName = "linkbackUri";
tableName = "Annotation";
- //TODO check non MySQL and with existing data (probably does not exist)
- step = ColumnNameChanger.NewClobInstance(stepName, tableName, columnName, newColumnName, INCLUDE_AUDIT);
+ // TODO check non MySQL and with existing data (probably does not exist)
+ step = ColumnNameChanger.NewClobInstance(stepName, tableName,
+ columnName, newColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //update Sicilia -> Sicily
- //#3540
+
+ // update Sicilia -> Sicily
+ // #3540
stepName = "Update Sicilia -> Sicily";
- query = " UPDATE Representation r " +
- " SET r.label = 'Sicily', r.text = 'Sicily' " +
- " WHERE (r.abbreviatedlabel = 'SIC-SI' OR r.abbreviatedlabel = 'SIC') AND r.label = 'Sicilia' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing("Representation");
+ query = " UPDATE Representation r "
+ + " SET r.label = 'Sicily', r.text = 'Sicily' "
+ + " WHERE (r.abbreviatedlabel = 'SIC-SI' OR r.abbreviatedlabel = 'SIC') AND r.label = 'Sicilia' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing("Representation");
stepList.add(step);
-
- //remove homotypical group form type designation base
+
+ // remove homotypical group form type designation base
stepName = "Remove column homotypical group in type designation base";
tableName = "TypeDesignationBase";
String oldColumnName = "homotypicalgroup_id";
- step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //add publish flag #1780
+
+ // add publish flag #1780
addPublishFlag(stepList);
-
- //add columns abbrevTitle, abbrevTitleCache and protectedAbbrevTitleCache to Reference
+
+ // add columns abbrevTitle, abbrevTitleCache and
+ // protectedAbbrevTitleCache to Reference
stepName = "Add abbrevTitle to Reference";
tableName = "Reference";
columnName = "abbrevTitle";
int length = 255;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Add abbrevTitleCache to Reference";
tableName = "Reference";
columnName = "abbrevTitleCache";
length = 1023;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Add protectedAbbrevTitleCache to Reference";
tableName = "Reference";
columnName = "protectedAbbrevTitleCache";
- step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false);
stepList.add(step);
-
- //update abbrevTitle, protectedAbbrevTitle and abbrevTitleCache in Reference
+
+ // update abbrevTitle, protectedAbbrevTitle and abbrevTitleCache in
+ // Reference
updateAbbrevTitle(stepList);
-
- //add doi to reference
+
+ // add doi to reference
stepName = "Add doi to Reference";
tableName = "Reference";
columnName = "doi";
length = 255;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
-
-
- //add start number to PolytomousKey
+
+ // add start number to PolytomousKey
stepName = "Add start number column to PolytomousKey";
tableName = "PolytomousKey";
columnName = "startNumber";
Integer defaultValue = 1;
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, defaultValue, true);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, defaultValue, true);
stepList.add(step);
-
- //add recordBasis to specimenOrObservationBase
+
+ // add recordBasis to specimenOrObservationBase
stepName = "Add recordBasis to SpecimenOrObservationBase";
tableName = "SpecimenOrObservationBase";
columnName = "recordBasis";
- length = 4; //TODO needed?
- //TODO NOT NULL
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ length = 4; // TODO needed?
+ // TODO NOT NULL
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
-
- //update recordBasis
+
+ // update recordBasis
updateRecordBasis(stepList);
-
- //update specimenOrObservationBase DTYPE with DerivedUnit where necessary
+
+ // update specimenOrObservationBase DTYPE with DerivedUnit where
+ // necessary
stepName = "Update Specimen -> DerivedUnit";
- query = " UPDATE SpecimenOrObservationBase sob " +
- " SET sob.DTYPE = 'DerivedUnit' " +
- " WHERE sob.DTYPE = 'Specimen' OR sob.DTYPE = 'Fossil' OR sob.DTYPE = 'LivingBeing' OR sob.DTYPE = 'Observation' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing("SpecimenOrObservationBase");
+ query = " UPDATE SpecimenOrObservationBase sob "
+ + " SET sob.DTYPE = 'DerivedUnit' "
+ + " WHERE sob.DTYPE = 'Specimen' OR sob.DTYPE = 'Fossil' OR sob.DTYPE = 'LivingBeing' OR sob.DTYPE = 'Observation' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing("SpecimenOrObservationBase");
stepList.add(step);
stepName = "Update Specimen -> DerivedUnit";
String newClass = "eu.etaxonomy.cdm.model.occurrence.DerivedUnit";
- String[] oldClassPaths = new String[]{
- "eu.etaxonomy.cdm.model.occurrence.Specimen"
- ,"eu.etaxonomy.cdm.model.occurrence.Fossil"
- ,"eu.etaxonomy.cdm.model.occurrence.LivingBeing"
- ,"eu.etaxonomy.cdm.model.occurrence.Observation"
- };
- step = ClassChanger.NewIdentifiableInstance(stepName, tableName, newClass, oldClassPaths, INCLUDE_AUDIT);
- stepList.add(step);
-
-
- //update DTYPE FieldObservation -> FieldUnit #3351
+ String[] oldClassPaths = new String[] {
+ "eu.etaxonomy.cdm.model.occurrence.Specimen",
+ "eu.etaxonomy.cdm.model.occurrence.Fossil",
+ "eu.etaxonomy.cdm.model.occurrence.LivingBeing",
+ "eu.etaxonomy.cdm.model.occurrence.Observation" };
+ step = ClassChanger.NewIdentifiableInstance(stepName, tableName,
+ newClass, oldClassPaths, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // update DTYPE FieldObservation -> FieldUnit #3351
stepName = "Update FieldObservation -> FieldUnit";
- query = " UPDATE SpecimenOrObservationBase sob " +
- " SET sob.DTYPE = 'FieldUnit' " +
- " WHERE sob.DTYPE = 'FieldObservation' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing("SpecimenOrObservationBase");
+ query = " UPDATE SpecimenOrObservationBase sob "
+ + " SET sob.DTYPE = 'FieldUnit' "
+ + " WHERE sob.DTYPE = 'FieldObservation' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing("SpecimenOrObservationBase");
stepList.add(step);
stepName = "Update Specimen -> DerivedUnit";
newClass = "eu.etaxonomy.cdm.model.occurrence.FieldUnit";
- oldClassPaths = new String[]{
- "eu.etaxonomy.cdm.model.occurrence.FieldObservation"
- };
- step = ClassChanger.NewIdentifiableInstance(stepName, tableName, newClass, oldClassPaths, INCLUDE_AUDIT);
+ oldClassPaths = new String[] { "eu.etaxonomy.cdm.model.occurrence.FieldObservation" };
+ step = ClassChanger.NewIdentifiableInstance(stepName, tableName,
+ newClass, oldClassPaths, INCLUDE_AUDIT);
stepList.add(step);
-
- //add kindOfUnit to SpecimenOrObservationBase
+
+ // add kindOfUnit to SpecimenOrObservationBase
stepName = "Add kindOfUnit column to SpecimenOrObservationBase";
tableName = "SpecimenOrObservationBase";
columnName = "kindOfUnit_id";
String relatedTable = "DefinedTermBase";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, relatedTable);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false, relatedTable);
stepList.add(step);
- //remove citation_id and citation micro-reference columns from Media table #2541
- //FIXME first check if columns are always empty
+ // remove citation_id and citation micro-reference columns from Media
+ // table #2541
+ // FIXME first check if columns are always empty
stepName = "Remove citation column from Media";
tableName = "Media";
columnName = "citation_id";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Remove citation microreference column from Media";
tableName = "Media";
columnName = "citationMicroReference";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //update length of all title caches and full title cache in names #1592
+
+ // update length of all title caches and full title cache in names #1592
updateTitleCacheLength(stepList);
-
- //rename FK column states_id -> stateData_id in DescriptionElementBase_StateData(+AUD) #2923
+
+ // rename FK column states_id -> stateData_id in
+ // DescriptionElementBase_StateData(+AUD) #2923
stepName = "Update states_id to stateData_id in DescriptionElementBase_StateData";
tableName = "DescriptionElementBase_StateData";
oldColumnName = "states_id";
newColumnName = "stateData_id";
- step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ step = ColumnNameChanger.NewIntegerInstance(stepName, tableName,
+ oldColumnName, newColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //specimen descriptions #3571
- //add column DescriptionBase.Specimen_ID #3571
+
+ // specimen descriptions #3571
+ // add column DescriptionBase.Specimen_ID #3571
stepName = "Add specimen_id column to DescriptionBase";
tableName = "DescriptionBase";
columnName = "specimen_id";
boolean notNull = false;
String referencedTable = "SpecimenOrObservationBase";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, notNull, referencedTable);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, notNull, referencedTable);
stepList.add(step);
-
- //update DescriptionBase.Specimen_ID data #3571
+
+ // update DescriptionBase.Specimen_ID data #3571
updateDescriptionSpecimenRelation(stepList);
- //remove tables DescriptionBase_SpecimenOrObservationBase(_AUD) #3571
+ // remove tables DescriptionBase_SpecimenOrObservationBase(_AUD) #3571
stepName = "Remove table DescriptionBase_SpecimenOrObservationBase";
tableName = "DescriptionBase_SpecimenOrObservationBase";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
- //change column type for reference type
- //TODO test with non-Mysql
+ // change column type for reference type
+ // TODO test with non-Mysql
stepName = "Change column type for Reference.type";
tableName = "Reference";
columnName = "refType";
Integer defaultValueStr = -1;
notNull = true;
int size = 3;
- step = ColumnTypeChanger.NewInt2StringInstance(stepName, tableName, columnName, size, true, defaultValueStr, notNull);
+ step = ColumnTypeChanger.NewInt2StringInstance(stepName, tableName,
+ columnName, size, true, defaultValueStr, notNull);
stepList.add(step);
-
- //update reference type
+
+ // update reference type
updateReferenceType(stepList);
-
- //create table CdmPreference #3555
+
+ // create table CdmPreference #3555
stepName = "Create table 'CdmPreference'";
tableName = "CdmPreference";
- TableCreator stepPref = TableCreator.NewInstance(stepName, tableName,
- new String[]{"key_subject", "key_predicate","value"}, //colNames
- new String[]{"string_100", "string_100","string_1023",}, // columnTypes
- new String[]{null, "DefinedTermBase",null}, //referencedTables
- ! INCLUDE_AUDIT, false);
+ TableCreator stepPref = TableCreator.NewInstance(stepName, tableName,
+ new String[] { "key_subject", "key_predicate", "value" }, // colNames
+ new String[] { "string_100", "string_100", "string_1023", }, // columnTypes
+ new String[] { null, "DefinedTermBase", null }, // referencedTables
+ !INCLUDE_AUDIT, false);
stepPref.setPrimaryKeyParams("key_subject, key_predicate", null);
stepList.add(stepPref);
- //FIXME length of key >= 1000
-
- //TODO fill CdmPreferences with default values
-
- //update RightsTerm to RightsType #1306
+ // FIXME length of key >= 1000
+
+ // TODO fill CdmPreferences with default values
+
+ // update RightsTerm to RightsType #1306
stepName = "Update RightsTerm -> RightsType";
String updateSql = "UPDATE DefinedTermBase SET DTYPE = 'RightsType' WHERE DTYPE = 'RightsTerm'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, updateSql).setDefaultAuditing("DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ updateSql).setDefaultAuditing("DefinedTermBase");
stepList.add(step);
-
- //update Rights table to RightsInfo
+
+ // update Rights table to RightsInfo
updateRights2RightsInfo(stepList);
-
- //Remove column isDescriptionSeparated from FeatureTree #3678
+
+ // Remove column isDescriptionSeparated from FeatureTree #3678
stepName = "Remove column isDescriptionSeparated from FeatureTree";
tableName = "FeatureTree";
columnName = "descriptionSeparated";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //remove table Sequence_GenBankAccession #3552
+
+ // remove table Sequence_GenBankAccession #3552
stepName = "Remove table Sequence_GenBankAccession";
tableName = "Sequence_GenBankAccession";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
-
- //remove table GenBankAccession #3552
+
+ // remove table GenBankAccession #3552
stepName = "Remove table GenBankAccession";
tableName = "GenBankAccession";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
-
- //remove table Sequence_Credit #3360
+
+ // remove table Sequence_Credit #3360
stepName = "Remove table Sequence_Credit";
tableName = "Sequence_Credit";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
- //remove table Sequence_Extension #3360
+ // remove table Sequence_Extension #3360
stepName = "Remove table Sequence_Extension";
tableName = "Sequence_Extension";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
- //remove table Sequence_OriginalSourceBase #3360
+ // remove table Sequence_OriginalSourceBase #3360
stepName = "Remove table Sequence_OriginalSourceBase";
tableName = "Sequence_OriginalSourceBase";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
- //remove table Sequence_OriginalSourceBase #3360
+ // remove table Sequence_OriginalSourceBase #3360
stepName = "Remove table Sequence_Rights";
tableName = "Sequence_Rights";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
-
- //remove old sequence columns
+
+ // remove old sequence columns
removeOldSequenceColumns(stepList);
-
- //add MediaSpecimen column #3614
+
+ // add MediaSpecimen column #3614
stepName = "Add mediaSpecimen column to SpecimenOrObservationBase";
tableName = "SpecimenOrObservationBase";
columnName = "mediaSpecimen_id";
notNull = false;
referencedTable = "Media";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, notNull, referencedTable);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, notNull, referencedTable);
stepList.add(step);
-
- //remove DescriptionBase_Feature #2202
+
+ // remove DescriptionBase_Feature #2202
stepName = "Remove table DescriptionBase_Feature";
tableName = "DescriptionBase_Feature";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
-
- //add timeperiod to columns to description element base #3312
- addTimeperiodToDescriptionElement(stepList);
+ // add timeperiod to columns to description element base #3312
+ addTimeperiodToDescriptionElement(stepList);
- //move specimen imdages
+ // move specimen imdages
stepName = "Move images from SpecimenOrObservationBase_Media to image gallery";
step = SpecimenMediaMoverUpdater.NewInstance();
stepList.add(step);
-
- //SpecimenOrObservationBase_Media #3597
+
+ // SpecimenOrObservationBase_Media #3597
stepName = "Remove table SpecimenOrObservationBase_Media";
tableName = "SpecimenOrObservationBase_Media";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
-
- //all molecular (#3360) and related updates
+
+ // all molecular (#3360) and related updates
updateMolecularAndRelated(stepList);
-
- //update vocabulary representaitons
+
+ // update vocabulary representaitons
step = TermVocabularyRepresentationUpdater.NewInstance();
stepList.add(step);
-
+
return stepList;
}
int length;
Integer defaultValue;
String referencedTable;
-
- //Primer #3360
+
+ // Primer #3360
stepName = "Create table 'Primer'";
tableName = "Primer";
- step = TableCreator.NewAnnotatableInstance(stepName, tableName,
- new String[]{"label","sequence_id","publishedIn_id"}, //colNames
- new String[]{"string_255","int","int"}, // columnTypes
- new String[]{null,Sequence.class.getSimpleName(),Reference.class.getSimpleName()}, //referencedTables
+ step = TableCreator.NewAnnotatableInstance(stepName, tableName,
+ new String[] { "label", "sequence_id", "publishedIn_id" }, // colNames
+ new String[] { "string_255", "int", "int" }, // columnTypes
+ new String[] { null, Sequence.class.getSimpleName(),
+ Reference.class.getSimpleName() }, // referencedTables
INCLUDE_AUDIT);
stepList.add(step);
-
- //MaterialOrMethod #3360
+
+ // MaterialOrMethod #3360
stepName = "Create table 'MaterialOrMethodEvent'";
tableName = MaterialOrMethodEvent.class.getSimpleName();
- step = TableCreator.NewEventInstance(stepName, tableName,
- new String[]{"DTYPE", "strain","temperature","definedMaterialOrMethod_id", "forwardPrimer_id","reversePrimer_id","medium_id"}, //colNames
- new String[]{"string_255", "string_255", "double", "int","int", "int", "int"}, // columnTypes
- new String[]{null, null, null, "DefinedTermBase","Primer","Primer","DefinedTermBase"}, //referencedTables
+ step = TableCreator.NewEventInstance(stepName, tableName, new String[] {
+ "DTYPE", "strain", "temperature", "definedMaterialOrMethod_id",
+ "forwardPrimer_id", "reversePrimer_id", "medium_id" }, // colNames
+ new String[] { "string_255", "string_255", "double", "int",
+ "int", "int", "int" }, // columnTypes
+ new String[] { null, null, null, "DefinedTermBase", "Primer",
+ "Primer", "DefinedTermBase" }, // referencedTables
INCLUDE_AUDIT);
stepList.add(step);
-
- stepName = "Remove preservation column from SpecimenOrObservationBase";
- //to fully remove all foreign keys, maybe there is a better way todo so
- //we don't expect any preservation information to exist in any CDM database
+
+ stepName = "Remove preservation column from SpecimenOrObservationBase";
+ // to fully remove all foreign keys, maybe there is a better way todo so
+ // we don't expect any preservation information to exist in any CDM
+ // database
tableName = "SpecimenOrObservationBase";
String oldColumnName = "preservation_id";
- step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- stepName = "Add new preservation column to SpecimenOrObservationBase";
+
+ stepName = "Add new preservation column to SpecimenOrObservationBase";
tableName = "SpecimenOrObservationBase";
String newColumnName = "preservation_id";
boolean notNull = false;
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, "MaterialOrMethodEvent");
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName,
+ newColumnName, INCLUDE_AUDIT, notNull, "MaterialOrMethodEvent");
stepList.add(step);
-
-
- //Amplification #3360
+
+ // Amplification #3360
stepName = "Create table 'Amplification'";
tableName = "Amplification";
- step = TableCreator.NewEventInstance(stepName, tableName,
- new String[]{"dnaSample_id","dnaMarker_id","forwardPrimer_id","reversePrimer_id","purification_id","cloning_id", "gelPhoto_id", "successful","successText","ladderUsed","electrophoresisVoltage","gelRunningTime","gelConcentration"}, //colNames
- new String[]{"int","int","int","int","int","int","int", "bit","string_255","string_255","double","double","double"}, // columnTypes
- new String[]{"SpecimenOrObservationBase","DefinedTermBase","Primer","Primer","MaterialOrMethodEvent", "MaterialOrMethodEvent", "Media", null, null, null, null, null, null}, //referencedTables
+ step = TableCreator.NewEventInstance(stepName, tableName,
+ new String[] { "dnaSample_id", "dnaMarker_id",
+ "forwardPrimer_id", "reversePrimer_id",
+ "purification_id", "cloning_id", "gelPhoto_id",
+ "successful", "successText", "ladderUsed",
+ "electrophoresisVoltage", "gelRunningTime",
+ "gelConcentration" }, // colNames
+ new String[] { "int", "int", "int", "int", "int", "int", "int",
+ "bit", "string_255", "string_255", "double", "double",
+ "double" }, // columnTypes
+ new String[] { "SpecimenOrObservationBase", "DefinedTermBase",
+ "Primer", "Primer", "MaterialOrMethodEvent",
+ "MaterialOrMethodEvent", "Media", null, null, null,
+ null, null, null }, // referencedTables
INCLUDE_AUDIT);
stepList.add(step);
-
- //SingleRead #3360
+
+ // SingleRead #3360
stepName = "Create table 'SingleRead'";
tableName = "SingleRead";
- step = TableCreator.NewEventInstance(stepName, tableName,
- new String[]{"amplification_id","materialOrMethod_id","primer_id","pherogram_id","direction","sequence_length"}, //colNames
- new String[]{"int","int","int","int","string_3","int"}, // columnTypes
- new String[]{"Amplification","MaterialOrMethodEvent", "Primer","Media", null, null}, //referencedTables
+ step = TableCreator.NewEventInstance(stepName, tableName, new String[] {
+ "amplification_id", "materialOrMethod_id", "primer_id",
+ "pherogram_id", "direction", "sequence_length" }, // colNames
+ new String[] { "int", "int", "int", "int", "string_3", "int" }, // columnTypes
+ new String[] { "Amplification", "MaterialOrMethodEvent",
+ "Primer", "Media", null, null }, // referencedTables
INCLUDE_AUDIT);
stepList.add(step);
-
- //sequence - consensussequence_string #3360
- stepName= "Add sequence_string to single read";
+
+ // sequence - consensussequence_string #3360
+ stepName = "Add sequence_string to single read";
columnName = "sequence_string";
- step = ColumnAdder.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
-
- //amplification - single reads #3360
- stepName= "Add single reads to amplification";
- String firstTable = "Amplification";
- String secondTable = "SingleRead";
- step = MnTableCreator.NewMnInstance(stepName, firstTable, null, secondTable, null, SchemaUpdaterBase.INCLUDE_AUDIT, false, true);
- stepList.add(step);
-
- //sequence - single reads #3360
- stepName= "Add single reads to sequence";
- firstTable = "Sequence";
- secondTable = "SingleRead";
- step = MnTableCreator.NewMnInstance(stepName, firstTable, null, secondTable, null, SchemaUpdaterBase.INCLUDE_AUDIT, false, true);
- stepList.add(step);
-
- //sequence - barcode #3360
- stepName= "Add barcodesequencepart_length to sequence";
+ step = ColumnAdder.NewClobInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // amplification - single reads #3360
+ stepName = "Add single reads to amplification";
+ String firstTable = "Amplification";
+ String secondTable = "SingleRead";
+ step = MnTableCreator
+ .NewMnInstance(stepName, firstTable, null, secondTable, null,
+ SchemaUpdaterBase.INCLUDE_AUDIT, false, true);
+ stepList.add(step);
+
+ // sequence - single reads #3360
+ stepName = "Add single reads to sequence";
+ firstTable = "Sequence";
+ secondTable = "SingleRead";
+ step = MnTableCreator
+ .NewMnInstance(stepName, firstTable, null, secondTable, null,
+ SchemaUpdaterBase.INCLUDE_AUDIT, false, true);
+ stepList.add(step);
+
+ // sequence - barcode #3360
+ stepName = "Add barcodesequencepart_length to sequence";
tableName = "Sequence";
columnName = "barcodeSequencePart_length";
defaultValue = null;
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, defaultValue, false);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, defaultValue, false);
stepList.add(step);
- //sequence - barcode #3360
- stepName= "Add barcodesequencepart_string to sequence";
+ // sequence - barcode #3360
+ stepName = "Add barcodesequencepart_string to sequence";
tableName = "Sequence";
columnName = "barcodeSequencePart_string";
- step = ColumnAdder.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnAdder.NewClobInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //sequence - consensussequence_length #3360
- stepName= "Add consensusSequence_length to sequence";
+
+ // sequence - consensussequence_length #3360
+ stepName = "Add consensusSequence_length to sequence";
tableName = "Sequence";
columnName = "consensusSequence_length";
defaultValue = null;
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, defaultValue, false);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, defaultValue, false);
stepList.add(step);
- //sequence - consensussequence_string #3360
- stepName= "Add consensusSequence_string to sequence";
+ // sequence - consensussequence_string #3360
+ stepName = "Add consensusSequence_string to sequence";
tableName = "Sequence";
columnName = "consensusSequence_string";
- step = ColumnAdder.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnAdder.NewClobInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //sequence - contigFile #3360
- stepName= "Add contigFile to sequence";
+
+ // sequence - contigFile #3360
+ stepName = "Add contigFile to sequence";
tableName = "Sequence";
columnName = "contigFile_id";
referencedTable = "Media";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, referencedTable);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false, referencedTable);
stepList.add(step);
-
- //sequence - boldprocessid #3360
- stepName= "Add boldprocessId to sequence";
+
+ // sequence - boldprocessid #3360
+ stepName = "Add boldprocessId to sequence";
tableName = "Sequence";
columnName = "boldProcessId";
length = 20;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
- //sequence - boldprocessid #3360
- stepName= "Add geneticAccessionNumber to sequence";
+ // sequence - boldprocessid #3360
+ stepName = "Add geneticAccessionNumber to sequence";
tableName = "Sequence";
columnName = "geneticAccessionNumber";
length = 20;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
-
- //sequence - haplotype #3360
- stepName= "Add haplotype to sequence";
+
+ // sequence - haplotype #3360
+ stepName = "Add haplotype to sequence";
tableName = "Sequence";
columnName = "haplotype";
length = 100;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ length, INCLUDE_AUDIT);
stepList.add(step);
- //sequence - isBarcode #3360
- stepName= "Add isBarcode to sequence";
+ // sequence - isBarcode #3360
+ stepName = "Add isBarcode to sequence";
tableName = "Sequence";
columnName = "isBarcode";
- step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false);
stepList.add(step);
-
- //sequence - dnaMarker #3360
- stepName= "Add dnaMarker to sequence";
+
+ // sequence - dnaMarker #3360
+ stepName = "Add dnaMarker to sequence";
tableName = "Sequence";
columnName = "dnaMarker_id";
referencedTable = "DefinedTermBase";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, referencedTable);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false, referencedTable);
stepList.add(step);
-
- //sequence - dnaSample #3360
- stepName= "Add dnaSample to sequence";
+
+ // sequence - dnaSample #3360
+ stepName = "Add dnaSample to sequence";
tableName = "Sequence";
columnName = "dnaSample_id";
referencedTable = "SpecimenOrObservationBase";
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, referencedTable);
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false, referencedTable);
stepList.add(step);
}
ISchemaUpdaterStep step;
String columnName;
String query;
-
- //TaxonBase
-
- //add publish flag to taxon
+
+ // TaxonBase
+
+ // add publish flag to taxon
stepName = "Add publish flag column to taxon base";
tableName = "TaxonBase";
columnName = "publish";
- step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, true);
+ step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, true);
stepList.add(step);
-
- //update publish with existing publish false markers
+
+ // update publish with existing publish false markers
stepName = "update TaxonBase publish if publish false markers exist";
- query = " UPDATE TaxonBase tb " +
- " SET publish = 0 " +
- " WHERE tb.id IN ( " +
- " SELECT DISTINCT MN.TaxonBase_id " +
- " FROM Marker m INNER JOIN TaxonBase_Marker MN ON MN.markers_id = m.id " +
- " INNER JOIN DefinedTermBase markerType ON m.markertype_id = markerType.id " +
- " WHERE m.flag = 0 AND markerType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonBase");
- stepList.add(step);
-
- //remove publish marker MN table
+ query = " UPDATE TaxonBase tb "
+ + " SET publish = 0 "
+ + " WHERE tb.id IN ( "
+ + " SELECT DISTINCT MN.TaxonBase_id "
+ + " FROM Marker m INNER JOIN TaxonBase_Marker MN ON MN.markers_id = m.id "
+ + " INNER JOIN DefinedTermBase markerType ON m.markertype_id = markerType.id "
+ + " WHERE m.flag = 0 AND markerType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query,
+ "TaxonBase");
+ stepList.add(step);
+
+ // remove publish marker MN table
stepName = "Remove existing TaxonBase publish markers MN";
- query = " DELETE " +
- " FROM TaxonBase_Marker " +
- " WHERE markers_id IN ( " +
- " SELECT m.id " +
- " FROM Marker m INNER JOIN DefinedTermBase mType ON m.markertype_id = mType.id " +
- " WHERE mType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonBase_Marker");
- stepList.add(step);
-
- //update publish with existing publish false markers
+ query = " DELETE "
+ + " FROM TaxonBase_Marker "
+ + " WHERE markers_id IN ( "
+ + " SELECT m.id "
+ + " FROM Marker m INNER JOIN DefinedTermBase mType ON m.markertype_id = mType.id "
+ + " WHERE mType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query,
+ "TaxonBase_Marker");
+ stepList.add(step);
+
+ // update publish with existing publish false markers
stepName = "Remove existing TaxonBase publish markers";
- query = " DELETE " +
- " FROM Marker " +
- " WHERE id NOT IN " +
- " (SELECT MN.markers_id FROM TaxonBase_Marker MN) " +
- " AND (markedObj_type = 'eu.etaxonomy.cdm.model.taxon.Synonym' OR markedObj_type = 'eu.etaxonomy.cdm.model.taxon.Taxon') " +
- " AND markertype_id IN ( " +
- "SELECT id FROM DefinedTermBase WHERE uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query); //AUD does not have markedObj_type
- stepList.add(step);
-
- //SpecimenOrObservationBase
-
- //add publish flag to specimen
+ query = " DELETE "
+ + " FROM Marker "
+ + " WHERE id NOT IN "
+ + " (SELECT MN.markers_id FROM TaxonBase_Marker MN) "
+ + " AND (markedObj_type = 'eu.etaxonomy.cdm.model.taxon.Synonym' OR markedObj_type = 'eu.etaxonomy.cdm.model.taxon.Taxon') "
+ + " AND markertype_id IN ( "
+ + "SELECT id FROM DefinedTermBase WHERE uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query); // AUD
+ // does
+ // not
+ // have
+ // markedObj_type
+ stepList.add(step);
+
+ // SpecimenOrObservationBase
+
+ // add publish flag to specimen
stepName = "Add publish flag column to SpecimenOrObservationBase";
tableName = "SpecimenOrObservationBase";
columnName = "publish";
- step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, true);
+ step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, true);
stepList.add(step);
-
- //update publish with existing publish false markers
+
+ // update publish with existing publish false markers
stepName = "update SpecimenOrObservationBase publish if publish false markers exist";
- query = " UPDATE SpecimenOrObservationBase sob " +
- " SET publish = 0 " +
- " WHERE sob.id IN ( " +
- " SELECT DISTINCT MN.SpecimenOrObservationBase_id " +
- " FROM Marker m INNER JOIN SpecimenOrObservationBase_Marker MN ON MN.markers_id = m.id " +
- " INNER JOIN DefinedTermBase markerType ON m.markertype_id = markerType.id " +
- " WHERE m.flag = 0 AND markerType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "SpecimenOrObservationBase");
- stepList.add(step);
-
- //remove publish marker MN table
+ query = " UPDATE SpecimenOrObservationBase sob "
+ + " SET publish = 0 "
+ + " WHERE sob.id IN ( "
+ + " SELECT DISTINCT MN.SpecimenOrObservationBase_id "
+ + " FROM Marker m INNER JOIN SpecimenOrObservationBase_Marker MN ON MN.markers_id = m.id "
+ + " INNER JOIN DefinedTermBase markerType ON m.markertype_id = markerType.id "
+ + " WHERE m.flag = 0 AND markerType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query,
+ "SpecimenOrObservationBase");
+ stepList.add(step);
+
+ // remove publish marker MN table
stepName = "Remove existing SpecimenOrObservationBase publish markers MN";
- query = " DELETE " +
- " FROM SpecimenOrObservationBase_Marker " +
- " WHERE markers_id IN ( " +
- " SELECT m.id " +
- " FROM Marker m INNER JOIN DefinedTermBase mType ON m.markertype_id = mType.id " +
- " WHERE mType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "SpecimenOrObservationBase_Marker");
- stepList.add(step);
-
- //update publish with existing publish false markers
+ query = " DELETE "
+ + " FROM SpecimenOrObservationBase_Marker "
+ + " WHERE markers_id IN ( "
+ + " SELECT m.id "
+ + " FROM Marker m INNER JOIN DefinedTermBase mType ON m.markertype_id = mType.id "
+ + " WHERE mType.uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query,
+ "SpecimenOrObservationBase_Marker");
+ stepList.add(step);
+
+ // update publish with existing publish false markers
stepName = "Remove existing SpecimenOrObservationBase publish markers";
- query = " DELETE " +
- " FROM Marker " +
- " WHERE id NOT IN " +
- " (SELECT MN.markers_id FROM SpecimenOrObservationBase_Marker MN) " +
- " AND (markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.DerivedUnit' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.FieldObservation' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.FieldUnit' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.Specimen' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.Fossil' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.LivingBeing' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.Observation' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.MediaSpecimen' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.TissueSample' " +
- "OR markedObj_type = 'eu.etaxonomy.cdm.model.molecular.DnaSample') " +
- " AND markertype_id IN ( " +
- "SELECT id FROM DefinedTermBase WHERE uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
+ query = " DELETE "
+ + " FROM Marker "
+ + " WHERE id NOT IN "
+ + " (SELECT MN.markers_id FROM SpecimenOrObservationBase_Marker MN) "
+ + " AND (markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.DerivedUnit' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.FieldObservation' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.FieldUnit' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.Specimen' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.Fossil' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.LivingBeing' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.Observation' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.MediaSpecimen' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.occurrence.TissueSample' "
+ + "OR markedObj_type = 'eu.etaxonomy.cdm.model.molecular.DnaSample') "
+ + " AND markertype_id IN ( "
+ + "SELECT id FROM DefinedTermBase WHERE uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query);
stepList.add(step);
-
- //remove all audited markers if no current markers exist
- //this may remove more audited markers then expected but we do accept this here
- stepName = "Remove all audited markers if no current markers exist";
- query = " DELETE " +
- " FROM Marker_AUD " +
- " WHERE id NOT IN (SELECT id FROM Marker ) " +
- " AND markertype_id IN ( " +
- "SELECT id FROM DefinedTermBase WHERE uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' " +
- ")" ;
+
+ // remove all audited markers if no current markers exist
+ // this may remove more audited markers then expected but we do accept
+ // this here
+ stepName = "Remove all audited markers if no current markers exist";
+ query = " DELETE "
+ + " FROM Marker_AUD "
+ + " WHERE id NOT IN (SELECT id FROM Marker ) "
+ + " AND markertype_id IN ( "
+ + "SELECT id FROM DefinedTermBase WHERE uuid = '0522c2b3-b21c-400c-80fc-a251c3501dbc' "
+ + ")";
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query);
stepList.add(step);
-
+
}
-
+
private void updateRights2RightsInfo(List<ISchemaUpdaterStep> stepList) {
- //#2945
+ // #2945
String stepName = "Update Rights to RightsInfo";
String tableName = "Rights";
String newTableName = "RightsInfo";
- ISchemaUpdaterStep step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ ISchemaUpdaterStep step = TableNameChanger.NewInstance(stepName,
+ tableName, newTableName, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update AgentBase_Rights to RightsInfo";
tableName = "AgentBase_Rights";
newTableName = "AgentBase_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Rights_Annotation to RightsInfo";
tableName = "Rights_Annotation";
newTableName = "RightsInfo_Annotation";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Rights_id column in RightsInfo_Annotation";
tableName = "RightsInfo_Annotation";
String columnName = "Rights_Id";
String newColumnName = "RightsInfo_id";
- step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, columnName, newColumnName, INCLUDE_AUDIT);
+ step = ColumnNameChanger.NewIntegerInstance(stepName, tableName,
+ columnName, newColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Rights_Marker to RightsInfo";
tableName = "Rights_Marker";
newTableName = "RightsInfo_Marker";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
stepName = "Update Rights_id column in RightsInfo_Marker";
tableName = "RightsInfo_Marker";
columnName = "Rights_Id";
newColumnName = "RightsInfo_id";
- step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, columnName, newColumnName, INCLUDE_AUDIT);
+ step = ColumnNameChanger.NewIntegerInstance(stepName, tableName,
+ columnName, newColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Classification_Rights to RightsInfo";
tableName = "Classification_Rights";
newTableName = "Classification_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Collection_Rights to RightsInfo";
tableName = "Collection_Rights";
newTableName = "Collection_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
stepName = "Update DefinedTermBase_Rights to RightsInfo";
tableName = "DefinedTermBase_Rights";
newTableName = "DefinedTermBase_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update DescriptionBase_Rights to RightsInfo";
tableName = "DescriptionBase_Rights";
newTableName = "DescriptionBase_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update FeatureTree_Rights to RightsInfo";
tableName = "FeatureTree_Rights";
newTableName = "FeatureTree_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Media_Rights to RightsInfo";
tableName = "Media_Rights";
newTableName = "Media_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update PolytomousKey_Rights to RightsInfo";
tableName = "PolytomousKey_Rights";
newTableName = "PolytomousKey_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update Reference_Rights to RightsInfo";
tableName = "Reference_Rights";
newTableName = "Reference_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update SpecimenOrObservationBase_Rights to RightsInfo";
tableName = "SpecimenOrObservationBase_Rights";
newTableName = "SpecimenOrObservationBase_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update TaxonBase_Rights to RightsInfo";
tableName = "TaxonBase_Rights";
newTableName = "TaxonBase_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update TaxonNameBase_Rights to RightsInfo";
tableName = "TaxonNameBase_Rights";
newTableName = "TaxonNameBase_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update TermVocabulary_Rights to RightsInfo";
tableName = "TermVocabulary_Rights";
newTableName = "TermVocabulary_RightsInfo";
- step = TableNameChanger.NewInstance(stepName, tableName, newTableName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, tableName, newTableName,
+ INCLUDE_AUDIT);
stepList.add(step);
}
private void updateReferenceType(List<ISchemaUpdaterStep> stepList) {
-
- String baseQuery = " UPDATE Reference " +
- " SET refType = '%s' " +
- " WHERE refType = '%s' ";
+
+ String baseQuery = " UPDATE Reference " + " SET refType = '%s' "
+ + " WHERE refType = '%s' ";
Integer index = 0;
String tableName = "Reference";
-
- //0-Article
+
+ // 0-Article
String stepName = "Update reference refType for Article";
- String query = String.format(baseQuery, ReferenceType.Article.getKey(), String.valueOf(index++));
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ String query = String.format(baseQuery, ReferenceType.Article.getKey(),
+ String.valueOf(index++));
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName);
stepList.add(step);
- //1-Book
+ // 1-Book
stepName = "Update reference refType for Book";
- query = String.format(baseQuery, ReferenceType.Book.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.Book.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //2-Book Section
+ // 2-Book Section
stepName = "Update reference refType for Book Section";
- query = String.format(baseQuery, ReferenceType.BookSection.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.BookSection.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //3-CD / DVD
+ // 3-CD / DVD
stepName = "Update reference refType for CD";
- query = String.format(baseQuery, ReferenceType.CdDvd.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.CdDvd.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //4-Database
+ // 4-Database
stepName = "Update reference refType for Database";
- query = String.format(baseQuery, ReferenceType.Database.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.Database.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //5-Generic
+ // 5-Generic
stepName = "Update reference refType for Generic";
- query = String.format(baseQuery, ReferenceType.Generic.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.Generic.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //6-InProceedings
+ // 6-InProceedings
stepName = "Update reference refType for InProceedings";
- query = String.format(baseQuery, ReferenceType.InProceedings.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.InProceedings.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //7-Journal
+ // 7-Journal
stepName = "Update reference refType for Journal";
- query = String.format(baseQuery, ReferenceType.Journal.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.Journal.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //8-Map
+
+ // 8-Map
stepName = "Update reference refType for Map";
- query = String.format(baseQuery, ReferenceType.Map.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.Map.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //9-Patent
+
+ // 9-Patent
stepName = "Update reference refType for Patent";
- query = String.format(baseQuery, ReferenceType.Patent.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.Patent.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //10-Personal Communication
+
+ // 10-Personal Communication
stepName = "Update reference refType for Personal Communication";
- query = String.format(baseQuery, ReferenceType.PersonalCommunication.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery,
+ ReferenceType.PersonalCommunication.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //11-PrintSeries
+
+ // 11-PrintSeries
stepName = "Update reference refType for PrintSeries";
- query = String.format(baseQuery, ReferenceType.PrintSeries.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format(baseQuery, ReferenceType.PrintSeries.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //12-Proceedings
+
+ // 12-Proceedings
stepName = "Update reference refType for Proceedings";
- query = String.format(baseQuery, ReferenceType.Proceedings.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);;
+ query = String.format(baseQuery, ReferenceType.Proceedings.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ ;
stepList.add(step);
-
- //13-Report
+
+ // 13-Report
stepName = "Update reference refType for Report";
- query = String.format(baseQuery, ReferenceType.Report.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);;
+ query = String.format(baseQuery, ReferenceType.Report.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ ;
stepList.add(step);
-
- //14-Thesis
+
+ // 14-Thesis
stepName = "Update reference refType for Thesis";
- query = String.format(baseQuery, ReferenceType.Thesis.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);;
+ query = String.format(baseQuery, ReferenceType.Thesis.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ ;
stepList.add(step);
- //15-WebPage
+ // 15-WebPage
stepName = "Update reference refType for WebPage";
- query = String.format(baseQuery, ReferenceType.WebPage.getKey(), String.valueOf(index++));
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);;
+ query = String.format(baseQuery, ReferenceType.WebPage.getKey(),
+ String.valueOf(index++));
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ ;
stepList.add(step);
}
private void updateRecordBasis(List<ISchemaUpdaterStep> stepList) {
String stepName = "Update recordBasis for SpecimenOrObservationBase";
String tableName = "SpecimenOrObservationBase";
-
- //Field Unit
- String query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.FieldUnit.getKey() + "' " +
- " WHERE DTYPE = 'FieldUnit' OR DTYPE = 'FieldObservation'";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //DerivedUnit
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.DerivedUnit.getKey() + "' " +
- " WHERE DTYPE = '" + DerivedUnit.class.getSimpleName() + "'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Living Being
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.LivingSpecimen.getKey() + "' " +
- " WHERE DTYPE = 'LivingBeing'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Observation
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.Observation.getKey() + "' " +
- " WHERE DTYPE = 'Observation'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Preserved Specimen
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.PreservedSpecimen.getKey() + "' " +
- " WHERE DTYPE = 'Specimen'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Fossil
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.Fossil.getKey() + "' " +
- " WHERE DTYPE = 'Fossil'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //DnaSample
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.DnaSample.getKey() + "' " +
- " WHERE DTYPE = 'DnaSample'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Unknown as default (if not yet handled before)
- query = " UPDATE " + tableName +
- " SET recordBasis = '" + SpecimenOrObservationType.Unknown.getKey() + "' " +
- " WHERE recordBasis IS NULL ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+
+ // Field Unit
+ String query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.FieldUnit.getKey() + "' "
+ + " WHERE DTYPE = 'FieldUnit' OR DTYPE = 'FieldObservation'";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName);
+ stepList.add(step);
+
+ // DerivedUnit
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.DerivedUnit.getKey() + "' "
+ + " WHERE DTYPE = '" + DerivedUnit.class.getSimpleName() + "'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // Living Being
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.LivingSpecimen.getKey() + "' "
+ + " WHERE DTYPE = 'LivingBeing'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // Observation
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.Observation.getKey() + "' "
+ + " WHERE DTYPE = 'Observation'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // Preserved Specimen
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.PreservedSpecimen.getKey() + "' "
+ + " WHERE DTYPE = 'Specimen'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // Fossil
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.Fossil.getKey() + "' "
+ + " WHERE DTYPE = 'Fossil'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // DnaSample
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.DnaSample.getKey() + "' "
+ + " WHERE DTYPE = 'DnaSample'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // Unknown as default (if not yet handled before)
+ query = " UPDATE " + tableName + " SET recordBasis = '"
+ + SpecimenOrObservationType.Unknown.getKey() + "' "
+ + " WHERE recordBasis IS NULL ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
}
- //update length of all title caches and full title cache in names
- //TODO test for H2, Postgres, SqlServer
- //https://dev.e-taxonomy.eu/trac/ticket/1592
- private void updateTitleCacheLength(List<ISchemaUpdaterStep> stepList) {
+ // update length of all title caches and full title cache in names
+ // TODO test for H2, Postgres, SqlServer
+ // https://dev.e-taxonomy.eu/trac/ticket/1592
+ private void updateTitleCacheLength(List<ISchemaUpdaterStep> stepList) {
String stepName;
String tableName;
ISchemaUpdaterStep step;
String columnName;
int size = 800;
-
+
stepName = "Change length of TaxonNameBase fullTitleCache";
tableName = "TaxonNameBase";
columnName = "fullTitleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of TaxonNameBase title cache";
tableName = "TaxonNameBase";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Change length of TaxonBase title cache";
tableName = "TaxonNameBase";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of Classification title cache";
tableName = "Classification";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of DescriptionBase title cache";
tableName = "DescriptionBase";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of FeatureTree title cache";
tableName = "FeatureTree";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of Collection title cache";
tableName = "Collection";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of Reference title cache";
tableName = "Reference";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of Media title cache";
tableName = "Media";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of PolytomousKey title cache";
tableName = "PolytomousKey";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of SpecimenOrObservationBase title cache";
tableName = "SpecimenOrObservationBase";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Change length of DefinedTermBase title cache";
tableName = "DefinedTermBase";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Change length of TermVocabulary title cache";
tableName = "TermVocabulary";
columnName = "titleCache";
- step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName, columnName, size , INCLUDE_AUDIT);
- stepList.add(step);
-
- }
-
-
- private void updateDescriptionSpecimenRelation(List<ISchemaUpdaterStep> stepList) {
- //TODO warn if multiple entries for 1 description exists
- String sqlCount = " SELECT count(*) as n " +
- " FROM DescriptionBase_SpecimenOrObservationBase MN " +
- " GROUP BY MN.descriptions_id " +
- " HAVING count(*) > 1 " +
- " ORDER BY MN.descriptions_id, MN.describedspecimenorobservations_id ";
-
- //TODO ... and log the concrete records
-// FROM DescriptionBase_SpecimenOrObservationBase ds
-// WHERE ds.descriptions_id IN (
-// SELECT MN.descriptions_id
-// FROM DescriptionBase_SpecimenOrObservationBase MN
-// GROUP BY MN.descriptions_id
-// HAVING count(*) > 1
-// )
-// ORDER BY descriptions_id, describedspecimenorobservations_id
-
- //TODO test for H2, Postgresql AND SQLServer (later will need TOP 1)
+ step = ColumnTypeChanger.NewStringSizeInstance(stepName, tableName,
+ columnName, size, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ }
+
+ private void updateDescriptionSpecimenRelation(
+ List<ISchemaUpdaterStep> stepList) {
+ // TODO warn if multiple entries for 1 description exists
+ String sqlCount = " SELECT count(*) as n "
+ + " FROM DescriptionBase_SpecimenOrObservationBase MN "
+ + " GROUP BY MN.descriptions_id "
+ + " HAVING count(*) > 1 "
+ + " ORDER BY MN.descriptions_id, MN.describedspecimenorobservations_id ";
+
+ // TODO ... and log the concrete records
+ // FROM DescriptionBase_SpecimenOrObservationBase ds
+ // WHERE ds.descriptions_id IN (
+ // SELECT MN.descriptions_id
+ // FROM DescriptionBase_SpecimenOrObservationBase MN
+ // GROUP BY MN.descriptions_id
+ // HAVING count(*) > 1
+ // )
+ // ORDER BY descriptions_id, describedspecimenorobservations_id
+
+ // TODO test for H2, Postgresql AND SQLServer (later will need TOP 1)
String stepName = "UPDATE Description - Specimen relation data ";
- String sql = " UPDATE DescriptionBase db " +
- " SET db.specimen_id = " +
- " (SELECT MN.describedspecimenorobservations_id " +
- " FROM DescriptionBase_SpecimenOrObservationBase MN " +
- " WHERE MN.descriptions_id = db.id " +
- " LIMIT 1 " +
- ")";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, sql);
- stepList.add(step);
-
+ String sql = " UPDATE DescriptionBase db " + " SET db.specimen_id = "
+ + " (SELECT MN.describedspecimenorobservations_id "
+ + " FROM DescriptionBase_SpecimenOrObservationBase MN "
+ + " WHERE MN.descriptions_id = db.id " + " LIMIT 1 " + ")";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, sql);
+ stepList.add(step);
+
}
private void updateAbbrevTitle(List<ISchemaUpdaterStep> stepList) {
String tableName = "Reference";
-
+
String stepName = "Update abbrevTitleCache for protected title caches with title";
- String query = " UPDATE Reference r " +
- " SET r.abbrevTitle = r.title, r.abbrevTitleCache = r.titleCache, r.protectedAbbrevTitleCache = r.protectedTitleCache";
-// + " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 1 ";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
-// stepName = "Update abbrevTitleCache for protected title caches with no title";
-// query = " UPDATE Reference r " +
-// " SET r.abbrevTitleCache = r.titleCache, r.protectedAbbrevTitleCache = r.protectedTitleCache" +
-// " WHERE r.title IS NULL AND r.protectedTitleCache = 1 ";
-// step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setAuditing("Reference");
-// stepList.add(step);
-
-// stepName = "Update abbrevTitleCache for protected title caches with title";
-// query = " UPDATE Reference r " +
-// " SET r.abbrevTitle = r.title, r.abbrevTitleCache = r.titleCache, r.protectedAbbrevTitleCache = r.protectedTitleCache" +
-// " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 0 ";
-// step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setAuditing("Reference");
-// stepList.add(step);
-
+ String query = " UPDATE Reference r "
+ + " SET r.abbrevTitle = left(r.title, 255), r.abbrevTitleCache = r.titleCache, r.protectedAbbrevTitleCache = r.protectedTitleCache";
+ // + " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 1 ";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName);
+ stepList.add(step);
+
+ // stepName =
+ // "Update abbrevTitleCache for protected title caches with no title";
+ // query = " UPDATE Reference r " +
+ // " SET r.abbrevTitleCache = r.titleCache, r.protectedAbbrevTitleCache = r.protectedTitleCache"
+ // +
+ // " WHERE r.title IS NULL AND r.protectedTitleCache = 1 ";
+ // step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ // query).setAuditing("Reference");
+ // stepList.add(step);
+
+ // stepName =
+ // "Update abbrevTitleCache for protected title caches with title";
+ // query = " UPDATE Reference r " +
+ // " SET r.abbrevTitle = r.title, r.abbrevTitleCache = r.titleCache, r.protectedAbbrevTitleCache = r.protectedTitleCache"
+ // +
+ // " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 0 ";
+ // step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ // query).setAuditing("Reference");
+ // stepList.add(step);
+
stepName = "Update reference title, set null where abbrev title very likely";
- query = " UPDATE Reference r " +
- " SET r.title = NULL " +
- " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 0 AND " +
- " ( LENGTH(r.title) <= 15 AND title like '%.%.%' OR LENGTH(r.title) < 30 AND title like '%.%.%.%' OR LENGTH(r.title) < 45 AND title like '%.%.%.%.%' OR LENGTH(r.title) < 60 AND title like '%.%.%.%.%.%' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = " UPDATE Reference r "
+ + " SET r.title = NULL "
+ + " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 0 AND "
+ + " ( LENGTH(r.title) <= 15 AND title like '%.%.%' OR LENGTH(r.title) < 30 AND title like '%.%.%.%' OR LENGTH(r.title) < 45 AND title like '%.%.%.%.%' OR LENGTH(r.title) < 60 AND title like '%.%.%.%.%.%' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
stepName = "Update reference abbrevTitle, set null where abbrev title very unlikely";
- query = " UPDATE Reference r " +
- " SET r.abbrevTitle = NULL " +
- " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 0 AND " +
- " ( title NOT like '%.%' OR LENGTH(r.title) > 30 AND title NOT like '%.%.%' " +
- ")" ;
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
+ query = " UPDATE Reference r "
+ + " SET r.abbrevTitle = NULL "
+ + " WHERE r.title IS NOT NULL AND r.protectedTitleCache = 0 AND "
+ + " ( title NOT like '%.%' OR LENGTH(r.title) > 30 AND title NOT like '%.%.%' "
+ + ")";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
}
private void removeOldSequenceColumns(List<ISchemaUpdaterStep> stepList) {
- //remove citation microreference
+ // remove citation microreference
String stepName = "Remove citationmicroreference column";
String tableName = "Sequence";
String columnName = "citationMicroReference";
- ISchemaUpdaterStep step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ ISchemaUpdaterStep step = ColumnRemover.NewInstance(stepName,
+ tableName, columnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //remove datesequenced
+
+ // remove datesequenced
stepName = "Remove datesequenced column";
columnName = "datesequenced";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //remove length
+
+ // remove length
stepName = "Remove length column";
columnName = "length";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //remove sequence
+
+ // remove sequence
stepName = "Remove sequence column";
columnName = "sequence";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
- //remove locus_id
+ // remove locus_id
stepName = "Remove locus_id column";
columnName = "locus_id";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //remove publishedin_id
+
+ // remove publishedin_id
stepName = "Remove publishedin_id column";
columnName = "publishedin_id";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
-
- //remove barcode
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // remove barcode
stepName = "Remove barcode column";
columnName = "barcode";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
- //identifiable columns
- //remove lsid_authority
+ // identifiable columns
+ // remove lsid_authority
stepName = "Remove lsid_authority";
columnName = "lsid_authority";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
- //remove lsid_lsid
+ // remove lsid_lsid
stepName = "Remove lsid_lsid";
columnName = "lsid_lsid";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
-
- //remove lsid_namespace
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // remove lsid_namespace
stepName = "Remove lsid_namespace";
columnName = "lsid_namespace";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
- //remove lsid_object
+ // remove lsid_object
stepName = "Remove lsid_object";
columnName = "lsid_object";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
-
- //remove lsid_revision
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // remove lsid_revision
stepName = "Remove lsid_revision";
columnName = "lsid_revision";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
-
- //remove protectedTitleCache
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // remove protectedTitleCache
stepName = "Remove protectedTitleCache";
columnName = "protectedTitleCache";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
-
- //remove titleCache
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ // remove titleCache
stepName = "Remove titleCache";
columnName = "titleCache";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
- stepList.add(step);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
+ stepList.add(step);
-}
+ }
private void updateIdInVocabulary(List<ISchemaUpdaterStep> stepList) {
String tableName = "DefinedTermBase";
-
- String queryVocUuid = " UPDATE DefinedTermBase dtb INNER JOIN TermVocabulary voc ON voc.id = dtb.vocabulary_id" +
- " SET dtb.idInVocabulary = (SELECT abbreviatedlabel " +
- " FROM DefinedTermBase_Representation MN " +
- " INNER JOIN Representation r ON r.id = MN.representations_id " +
- " WHERE MN.DefinedTermBase_id = dtb.id) " +
- " WHERE voc.uuid = '%s'";
-
- //Languages (ISO)
+
+ String queryVocUuid = " UPDATE DefinedTermBase dtb INNER JOIN TermVocabulary voc ON voc.id = dtb.vocabulary_id"
+ + " SET dtb.idInVocabulary = (SELECT abbreviatedlabel "
+ + " FROM DefinedTermBase_Representation MN "
+ + " INNER JOIN Representation r ON r.id = MN.representations_id "
+ + " WHERE MN.DefinedTermBase_id = dtb.id) "
+ + " WHERE voc.uuid = '%s'";
+
+ // Languages (ISO)
String stepName = "Update idInVocabulary for Languages ";
- String query = "UPDATE DefinedTermBase dtb INNER JOIN TermVocabulary voc ON voc.id = dtb.vocabulary_id " +
- " SET dtb.idInVocabulary = dtb.iso639_2 "+
- " WHERE voc.uuid = '45ac7043-7f5e-4f37-92f2-3874aaaef2de' ";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName); //not fully correct as we should join with TermVoc_AUD but good enough for this usecase
+ String query = "UPDATE DefinedTermBase dtb INNER JOIN TermVocabulary voc ON voc.id = dtb.vocabulary_id "
+ + " SET dtb.idInVocabulary = dtb.iso639_2 "
+ + " WHERE voc.uuid = '45ac7043-7f5e-4f37-92f2-3874aaaef2de' ";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName); // not fully correct as we should join with
+ // TermVoc_AUD but good enough for this
+ // usecase
stepList.add(step);
- //Undefined Languages => all
+ // Undefined Languages => all
stepName = "Update idInVocabulary for undefined languages";
String uuid = "7fd1e6d0-2e76-4dfa-bad9-2673dd042c28";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Waterbody & Country => all
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // Waterbody & Country => all
stepName = "Update idInVocabulary for WaterbodyOrCountries";
uuid = "006b1870-7347-4624-990f-e5ed78484a1a";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //TdwgAreas => all
+
+ // TdwgAreas => all
stepName = "Update idInVocabulary for TDWG areas";
uuid = NamedArea.uuidTdwgAreaVocabulary.toString();
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //Rank => some
+
+ // Rank => some
stepName = "Update idInVocabulary for ranks";
uuid = "ef0d1ce1-26e3-4e83-b47b-ca74eed40b1b";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //avoid duplicate for section (bot.)
+
+ // avoid duplicate for section (bot.)
stepName = "Update idInVoc for section (bot.)";
String sql = " UPDATE DefinedTermBase SET idInVocabulary = 'sect.(bot.)' WHERE uuid = '3edff68f-8527-49b5-bf91-7e4398bb975c'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- //avoid duplicate for subsection (bot.)
+ // avoid duplicate for subsection (bot.)
stepName = "Update idInVoc for subsection (bot.)";
sql = " UPDATE DefinedTermBase SET idInVocabulary = 'subsect.(bot.)' WHERE uuid = 'd20f5b61-d463-4448-8f8a-c1ff1f262f59'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- //avoid duplicate for section (zool.)
+ // avoid duplicate for section (zool.)
stepName = "Update idInVoc for section (zool.)";
sql = " UPDATE DefinedTermBase SET idInVocabulary = 'sect.(zool.)' WHERE uuid = '691d371e-10d7-43f0-93db-3d7fa1a62c54'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- //avoid duplicate for subsection (zool.)
+ // avoid duplicate for subsection (zool.)
stepName = "Update idInVoc for subsection (zool.)";
sql = " UPDATE DefinedTermBase SET idInVocabulary = 'subsect.(zool.)' WHERE uuid = '0ed32d28-adc4-4303-a9ca-68e2acd67e33'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
-
- //SpecimenTypeDesignationStatus => all
+ // SpecimenTypeDesignationStatus => all
stepName = "Update idInVocabulary for SpecimenTypeDesignationStatus";
uuid = "ab177bd7-d3c8-4e58-a388-226fff6ba3c2";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //avoid duplicate for PT
+ // avoid duplicate for PT
stepName = "Update idInVoc for Phototype (PhT) to avoid duplicate for PT";
sql = " UPDATE DefinedTermBase SET idInVocabulary = 'PhT' WHERE uuid = 'b7807acc-f559-474e-ad4a-e7a41e085e34'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
-
- //NameTypeDesignationStatus => all
+
+ // NameTypeDesignationStatus => all
stepName = "Update idInVocabulary for NameTypeDesignationStatus";
uuid = "ab60e738-4d09-4c24-a1b3-9466b01f9f55";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //NomenclaturalStatusType => all, abbrevs.
+
+ // NomenclaturalStatusType => all, abbrevs.
stepName = "Update idInVocabulary for NomenclaturalStatusType";
uuid = "bb28cdca-2f8a-4f11-9c21-517e9ae87f1f";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //TaxonRelationshipType, all but 2 (Invalid Designation for, Misapplied Name for)
+ // TaxonRelationshipType, all but 2 (Invalid Designation for, Misapplied
+ // Name for)
stepName = "Update idInVocabulary for TaxonRelationshipType";
uuid = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //avoid duplicate for Misapplied Name (remove '-')
+
+ // avoid duplicate for Misapplied Name (remove '-')
stepName = "Update idInVoc for Misapplied Name Relationship";
sql = " UPDATE DefinedTermBase SET idInVocabulary = NULL WHERE uuid = '1ed87175-59dd-437e-959e-0d71583d8417'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
-
- //avoid duplicate for Invalid designation (remove '-')
+
+ // avoid duplicate for Invalid designation (remove '-')
stepName = "Update idInVoc for Invalid Designation";
sql = " UPDATE DefinedTermBase SET idInVocabulary = NULL WHERE uuid = '605b1d01-f2b1-4544-b2e0-6f08def3d6ed'";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
-
- //PresenceTerm => all
+
+ // PresenceTerm => all
stepName = "Update idInVocabulary for PresenceTerm";
uuid = "adbbbe15-c4d3-47b7-80a8-c7d104e53a05";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //AbsenceTerm => all
+ // AbsenceTerm => all
stepName = "Update idInVocabulary for AbsenceTerm";
uuid = "5cd438c8-a8a1-4958-842e-169e83e2ceee";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //Sex => all
+
+ // Sex => all
stepName = "Update idInVocabulary for Sex";
uuid = "9718b7dd-8bc0-4cad-be57-3c54d4d432fe";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //ExtensionType => all
+ // ExtensionType => all
stepName = "Update idInVocabulary for ExtensionType";
uuid = "117cc307-5bd4-4b10-9b2f-2e14051b3b20";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //ReferenceSystem => all
+ // ReferenceSystem => all
stepName = "Update idInVocabulary for ReferenceSystem";
uuid = "ec6376e5-0c9c-4f5c-848b-b288e6c17a86";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //DeterminationModifier => all
+
+ // DeterminationModifier => all
stepName = "Update idInVocabulary for DeterminationModifier";
uuid = "fe87ea8d-6e0a-4e5d-b0da-0ab8ea67ca77";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(queryVocUuid, uuid)).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName,
+ String.format(queryVocUuid, uuid))
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //InstitutionType, MeasurementUnit, Scope, Stage, State, TextFormat, Modifier, PreservationMethod => dummies
+ // InstitutionType, MeasurementUnit, Scope, Stage, State, TextFormat,
+ // Modifier, PreservationMethod => dummies
stepName = "Update idInVocabulary for dummy terms in several vocabularies";
- query = " UPDATE DefinedTermBase dtb " +
- " SET dtb.idInVocabulary = (SELECT abbreviatedlabel " +
- " FROM DefinedTermBase_Representation MN " +
- " INNER JOIN Representation r ON r.id = MN.representations_id " +
- " WHERE MN.DefinedTermBase_id = dtb.id) " +
- " WHERE dtb.termType IN ('%s','%s','%s','%s','%s','%s','%s','%s')";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, String.format(query,
- TermType.InstitutionType.getKey(), TermType.MeasurementUnit.getKey(),
- TermType.Scope.getKey(), TermType.Stage.getKey(), TermType.State.getKey(),
- TermType.TextFormat.getKey(), TermType.Modifier.getKey(), TermType.Method.getKey()))
- .setDefaultAuditing(tableName);
- stepList.add(step);
-
+ query = " UPDATE DefinedTermBase dtb "
+ + " SET dtb.idInVocabulary = (SELECT abbreviatedlabel "
+ + " FROM DefinedTermBase_Representation MN "
+ + " INNER JOIN Representation r ON r.id = MN.representations_id "
+ + " WHERE MN.DefinedTermBase_id = dtb.id) "
+ + " WHERE dtb.termType IN ('%s','%s','%s','%s','%s','%s','%s','%s')";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(
+ stepName,
+ String.format(query, TermType.InstitutionType.getKey(),
+ TermType.MeasurementUnit.getKey(),
+ TermType.Scope.getKey(), TermType.Stage.getKey(),
+ TermType.State.getKey(), TermType.TextFormat.getKey(),
+ TermType.Modifier.getKey(), TermType.Method.getKey()))
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
stepName = "Update idInVocabulary for dummy state";
- query = " UPDATE DefinedTermBase dtb " +
- " SET dtb.idinvocabulary = 'std' " +
- " WHERE dtb.uuid = '881b9c80-626d-47a6-b308-a63ee5f4178f' ";
+ query = " UPDATE DefinedTermBase dtb "
+ + " SET dtb.idinvocabulary = 'std' "
+ + " WHERE dtb.uuid = '881b9c80-626d-47a6-b308-a63ee5f4178f' ";
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query);
stepList.add(step);
stepName = "Update idInVocabulary for dummy stage";
- query = " UPDATE DefinedTermBase dtb " +
- " SET dtb.idinvocabulary = 'sgd' " +
- " WHERE dtb.uuid = '48f8e8a7-a2ac-4974-9ce8-6944afc5095e' ";
+ query = " UPDATE DefinedTermBase dtb "
+ + " SET dtb.idinvocabulary = 'sgd' "
+ + " WHERE dtb.uuid = '48f8e8a7-a2ac-4974-9ce8-6944afc5095e' ";
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query);
stepList.add(step);
stepName = "Update idInVocabulary for dummy modifier";
- query = " UPDATE DefinedTermBase dtb " +
- " SET dtb.idinvocabulary = 'md' " +
- " WHERE dtb.uuid = 'efc38dad-205c-4028-ad9d-ae509a14b37a' ";
+ query = " UPDATE DefinedTermBase dtb "
+ + " SET dtb.idinvocabulary = 'md' "
+ + " WHERE dtb.uuid = 'efc38dad-205c-4028-ad9d-ae509a14b37a' ";
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query);
stepList.add(step);
- //Remove state dummy
+ // Remove state dummy
stepName = "Remove state dummy if possible";
uuid = "881b9c80-626d-47a6-b308-a63ee5f4178f";
- String checkUsed = " SELECT count(*) as n FROM StateData sd " +
- " WHERE sd.state_id = %d ";
+ String checkUsed = " SELECT count(*) as n FROM StateData sd "
+ + " WHERE sd.state_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed);
stepList.add(step);
-
- //Remove institution type dummy
+
+ // Remove institution type dummy
stepName = "Remove institution type dummy term";
uuid = "bea94a6c-472b-421c-abc1-52f797c51dbf";
- checkUsed = " SELECT count(*) as n FROM AgentBase_DefinedTermBase MN " +
- " WHERE MN.types_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM AgentBase_DefinedTermBase MN "
+ + " WHERE MN.types_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed);
stepList.add(step);
- //Remove measurement unit dummy
+ // Remove measurement unit dummy
stepName = "Remove measurement unit dummy term";
uuid = "e19dd590-5be8-4c93-978f-b78554116289";
- checkUsed = " SELECT count(*) as n FROM DescriptionElementBase deb " +
- " WHERE deb.unit_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM DescriptionElementBase deb "
+ + " WHERE deb.unit_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed);
stepList.add(step);
-
- //Remove scope dummy
+
+ // Remove scope dummy
stepName = "Remove scope dummy term";
uuid = "2ace7f1f-4ce6-47e1-8a65-e3f6b724876c";
- checkUsed = " SELECT count(*) as n FROM DescriptionBase_Scope MN " +
- " WHERE MN.scopes_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM DescriptionBase_Scope MN "
+ + " WHERE MN.scopes_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed);
stepList.add(step);
-
- //Remove stage dummy
+
+ // Remove stage dummy
stepName = "Remove stage dummy term";
uuid = "48f8e8a7-a2ac-4974-9ce8-6944afc5095e";
- checkUsed = " SELECT count(*) as n FROM DescriptionBase_Scope MN " +
- " WHERE MN.scopes_id = %d ";
- String checkUsed2 = " SELECT count(*) as n FROM SpecimenOrObservationBase osb " +
- " WHERE osb.lifestage_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM DescriptionBase_Scope MN "
+ + " WHERE MN.scopes_id = %d ";
+ String checkUsed2 = " SELECT count(*) as n FROM SpecimenOrObservationBase osb "
+ + " WHERE osb.lifestage_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed)
.addCheckUsedQuery(checkUsed2);
stepList.add(step);
- //Remove text format dummy
+ // Remove text format dummy
stepName = "Remove text format dummy if possible";
uuid = "5d095782-d99c-46bc-a158-edb2e47c9b63";
- checkUsed = " SELECT count(*) as n FROM DescriptionElementBase deb " +
- " WHERE deb.format_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM DescriptionElementBase deb "
+ + " WHERE deb.format_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed);
stepList.add(step);
- //Remove modifier dummy
+ // Remove modifier dummy
stepName = "Remove modifier dummy if possible";
uuid = "efc38dad-205c-4028-ad9d-ae509a14b37a";
- checkUsed = " SELECT count(*) as n FROM DescriptionElementBase_Modifier MN " +
- " WHERE MN.modifiers_id = %d ";
- checkUsed2 = " SELECT count(*) as n FROM StateData_DefinedTermBase MN " +
- " WHERE MN.modifiers_id = %d ";
- String checkUsed3 = " SELECT count(*) as n FROM StatisticalMeasurementValue_DefinedTermBase MN " +
- " WHERE MN.modifiers_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM DescriptionElementBase_Modifier MN "
+ + " WHERE MN.modifiers_id = %d ";
+ checkUsed2 = " SELECT count(*) as n FROM StateData_DefinedTermBase MN "
+ + " WHERE MN.modifiers_id = %d ";
+ String checkUsed3 = " SELECT count(*) as n FROM StatisticalMeasurementValue_DefinedTermBase MN "
+ + " WHERE MN.modifiers_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed)
- .addCheckUsedQuery(checkUsed2)
- .addCheckUsedQuery(checkUsed3);
+ .addCheckUsedQuery(checkUsed2).addCheckUsedQuery(checkUsed3);
stepList.add(step);
-
- //Remove text preservation method dummy
+
+ // Remove text preservation method dummy
stepName = "Remove preservation method dummy if possible";
uuid = "3edc2633-365b-4a9b-bc3a-f3f85f59dbdf";
- checkUsed = " SELECT count(*) as n FROM SpecimenOrObservationBase osb " +
- " WHERE osb.preservation_id = %d ";
+ checkUsed = " SELECT count(*) as n FROM SpecimenOrObservationBase osb "
+ + " WHERE osb.preservation_id = %d ";
step = SingleTermRemover.NewInstance(stepName, uuid, checkUsed);
stepList.add(step);
-
- //Split Country Vocabulary #3700
+
+ // Split Country Vocabulary #3700
stepName = "Create Waterbody vocabulary";
- UUID uuidVocabulary = UUID.fromString("35a62b25-f541-4f12-a7c7-17d90dec3e03");
+ UUID uuidVocabulary = UUID
+ .fromString("35a62b25-f541-4f12-a7c7-17d90dec3e03");
String description = "Major Waterbodies of the World";
String label = "Waterbody";
String abbrev = null;
boolean isOrdered = false;
TermType termType = TermType.NamedArea;
Class<?> termClass = NamedArea.class;
- step = VocabularyCreator.NewVocabularyInstance(uuidVocabulary, description, label, abbrev, isOrdered, termClass, termType);
+ step = VocabularyCreator.NewVocabularyInstance(uuidVocabulary,
+ description, label, abbrev, isOrdered, termClass, termType);
stepList.add(step);
-
+
stepName = "Move waterbodies to new vocabulary";
- UUID newVocabulary = UUID.fromString("35a62b25-f541-4f12-a7c7-17d90dec3e03");
- step = TermMover.NewInstance(stepName, newVocabulary, "aa96ca19-46ab-6365-af29-e4842f13eb4c")
- .addTermUuid(UUID.fromString("36aea55c-46ab-6365-af29-e4842f13eb4c"))
- .addTermUuid(UUID.fromString("36aea55c-892c-6365-af29-e4842f13eb4c"))
- .addTermUuid(UUID.fromString("36aea55c-892c-4114-af29-d4b287f76fab"))
- .addTermUuid(UUID.fromString("aa96ca19-892c-4114-af29-d4b287f76fab"))
- .addTermUuid(UUID.fromString("aa96ca19-892c-4114-a494-d4b287f76fab"))
- .addTermUuid(UUID.fromString("d4cf6c57-892c-4114-bf57-96886eb7108a"))
- .addTermUuid(UUID.fromString("d4cf6c57-892c-c953-a494-96886eb7108a"))
- .addTermUuid(UUID.fromString("aa96ca19-46ab-c953-a494-96886eb7108a"))
- .addTermUuid(UUID.fromString("aa96ca19-46ab-4114-a494-96886eb7108a"))
- ;
- stepList.add(step);
-
- //update waterbody uuids #3705 AND waterbody DTYPE to NamedArea and sortindex new #3700
+ UUID newVocabulary = UUID
+ .fromString("35a62b25-f541-4f12-a7c7-17d90dec3e03");
+ step = TermMover
+ .NewInstance(stepName, newVocabulary,
+ "aa96ca19-46ab-6365-af29-e4842f13eb4c")
+ .addTermUuid(
+ UUID.fromString("36aea55c-46ab-6365-af29-e4842f13eb4c"))
+ .addTermUuid(
+ UUID.fromString("36aea55c-892c-6365-af29-e4842f13eb4c"))
+ .addTermUuid(
+ UUID.fromString("36aea55c-892c-4114-af29-d4b287f76fab"))
+ .addTermUuid(
+ UUID.fromString("aa96ca19-892c-4114-af29-d4b287f76fab"))
+ .addTermUuid(
+ UUID.fromString("aa96ca19-892c-4114-a494-d4b287f76fab"))
+ .addTermUuid(
+ UUID.fromString("d4cf6c57-892c-4114-bf57-96886eb7108a"))
+ .addTermUuid(
+ UUID.fromString("d4cf6c57-892c-c953-a494-96886eb7108a"))
+ .addTermUuid(
+ UUID.fromString("aa96ca19-46ab-c953-a494-96886eb7108a"))
+ .addTermUuid(
+ UUID.fromString("aa96ca19-46ab-4114-a494-96886eb7108a"));
+ stepList.add(step);
+
+ // update waterbody uuids #3705 AND waterbody DTYPE to NamedArea and
+ // sortindex new #3700
stepName = "Update waterbody uuids";
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 1, uuid = 'af4271e5-8897-4e6f-9db7-54ea4f28cfc0' WHERE uuid = 'aa96ca19-46ab-6365-af29-e4842f13eb4c' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 1, uuid = 'af4271e5-8897-4e6f-9db7-54ea4f28cfc0' WHERE uuid = 'aa96ca19-46ab-6365-af29-e4842f13eb4c' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 2, uuid = '77e79804-1b17-4c99-873b-933fe216e3da' WHERE uuid = '36aea55c-46ab-6365-af29-e4842f13eb4c' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 2, uuid = '77e79804-1b17-4c99-873b-933fe216e3da' WHERE uuid = '36aea55c-46ab-6365-af29-e4842f13eb4c' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 3, uuid = '3d68a327-104c-49d5-a2d8-c71c6600181b' WHERE uuid = '36aea55c-892c-6365-af29-e4842f13eb4c' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 3, uuid = '3d68a327-104c-49d5-a2d8-c71c6600181b' WHERE uuid = '36aea55c-892c-6365-af29-e4842f13eb4c' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 4, uuid = 'ff744a37-5990-462c-9c20-1e85a9943851' WHERE uuid = '36aea55c-892c-4114-af29-d4b287f76fab' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 4, uuid = 'ff744a37-5990-462c-9c20-1e85a9943851' WHERE uuid = '36aea55c-892c-4114-af29-d4b287f76fab' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 5, uuid = 'ef04f363-f67f-4a2c-8d98-110de4c5f654' WHERE uuid = 'aa96ca19-892c-4114-af29-d4b287f76fab' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 5, uuid = 'ef04f363-f67f-4a2c-8d98-110de4c5f654' WHERE uuid = 'aa96ca19-892c-4114-af29-d4b287f76fab' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 6, uuid = '8811a47e-29d6-4455-8f83-8916b78a692f' WHERE uuid = 'aa96ca19-892c-4114-a494-d4b287f76fab' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 6, uuid = '8811a47e-29d6-4455-8f83-8916b78a692f' WHERE uuid = 'aa96ca19-892c-4114-a494-d4b287f76fab' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 7, uuid = '4cb4bbae-9aab-426c-9025-e34f809165af' WHERE uuid = 'd4cf6c57-892c-4114-bf57-96886eb7108a' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 7, uuid = '4cb4bbae-9aab-426c-9025-e34f809165af' WHERE uuid = 'd4cf6c57-892c-4114-bf57-96886eb7108a' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 8, uuid = '598fec0e-b93a-4947-a1f3-601e380797f7' WHERE uuid = 'd4cf6c57-892c-c953-a494-96886eb7108a' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 8, uuid = '598fec0e-b93a-4947-a1f3-601e380797f7' WHERE uuid = 'd4cf6c57-892c-c953-a494-96886eb7108a' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 9, uuid = 'ee69385e-6c80-405c-be6e-974e9fd1e297' WHERE uuid = 'aa96ca19-46ab-c953-a494-96886eb7108a' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 9, uuid = 'ee69385e-6c80-405c-be6e-974e9fd1e297' WHERE uuid = 'aa96ca19-46ab-c953-a494-96886eb7108a' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
- sql =" UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 10, uuid = '8dc16e70-74b8-4143-95cf-a659a319a854' WHERE uuid = 'aa96ca19-46ab-4114-a494-96886eb7108a' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'NamedArea', orderindex = 10, uuid = '8dc16e70-74b8-4143-95cf-a659a319a854' WHERE uuid = 'aa96ca19-46ab-4114-a494-96886eb7108a' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
-
- //update DTYPE for country
+
+ // update DTYPE for country
stepName = "Update DTYPE for Countries";
- sql =" UPDATE DefinedTermBase SET DTYPE = 'Country' WHERE DTYPE = 'WaterbodyOrCountry' ";
- step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql, "DefinedTermBase");
+ sql = " UPDATE DefinedTermBase SET DTYPE = 'Country' WHERE DTYPE = 'WaterbodyOrCountry' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, sql,
+ "DefinedTermBase");
stepList.add(step);
-
- //Rename tables
+
+ // Rename tables
stepName = "Rename DefinedTermBase_WaterbodyOrCountry";
String oldName = "DefinedTermBase_WaterbodyOrCountry";
String newName = "DefinedTermBase_Country";
- step = TableNameChanger.NewInstance(stepName, oldName, newName, INCLUDE_AUDIT);
+ step = TableNameChanger.NewInstance(stepName, oldName, newName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //rename column
+
+ // rename column
stepName = "Rename DefinedTermBase_Country.waterbodiesorcountries_id";
tableName = "DefinedTermBase_Country";
String oldColumnName = "waterbodiesorcountries_id";
String newColumnName = "countries_id";
- step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ step = ColumnNameChanger.NewIntegerInstance(stepName, tableName,
+ oldColumnName, newColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //NULL for empty strings
+ // NULL for empty strings
stepName = "Update idInVocabulary, replace empty strings by null";
query = "Update DefinedTermBase dtb SET idInVocabulary = NULL WHERE idInVocabulary = ''";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //MarkerType, AnnotationType, NamedAreaType, NamedAreaLevel, Feature, Continent, DerivationEventType, StatisticalMeasure, RightsType,SynonymRelationshipType & HybridRelationshipType & NameRelationshipType
- //=> none
-
- //DnaMarker => yes but no entries
-
- //Clean up empty abbreviated labels in representations
+ // MarkerType, AnnotationType, NamedAreaType, NamedAreaLevel, Feature,
+ // Continent, DerivationEventType, StatisticalMeasure,
+ // RightsType,SynonymRelationshipType & HybridRelationshipType &
+ // NameRelationshipType
+ // => none
+
+ // DnaMarker => yes but no entries
+
+ // Clean up empty abbreviated labels in representations
stepName = "Update abbreviated label, replace empty strings by null";
query = "Update Representation r SET r.abbreviatedLabel = NULL WHERE r.abbreviatedLabel = ''";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing("Representation"); //AUD not needed
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing("Representation"); // AUD not needed
stepList.add(step);
}
- private void updateTermTypesForVocabularies( List<ISchemaUpdaterStep> stepList) {
- //vocabularies with terms
- for (TermType termType : TermType.values()){
+ private void updateTermTypesForVocabularies(
+ List<ISchemaUpdaterStep> stepList) {
+ // vocabularies with terms
+ for (TermType termType : TermType.values()) {
updateTermTypeForVocabularies(stepList, termType);
}
-
+
String tableName = "TermVocabulary";
- //Natural Language Terms
+ // Natural Language Terms
String stepName = "Updater termType for NaturalLanguageTerms";
- String query = "UPDATE TermVocabulary voc " +
- " SET voc.termType = '" + TermType.NaturalLanguageTerm.getKey() + "' " +
- " WHERE voc.uuid = 'fdaba4b0-5c14-11df-a08a-0800200c9a66'";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ String query = "UPDATE TermVocabulary voc " + " SET voc.termType = '"
+ + TermType.NaturalLanguageTerm.getKey() + "' "
+ + " WHERE voc.uuid = 'fdaba4b0-5c14-11df-a08a-0800200c9a66'";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName);
stepList.add(step);
- //remaining vocabularies
+ // remaining vocabularies
stepName = "Updater termType for remaining vocabularies";
- query = "UPDATE TermVocabulary voc " +
- " SET voc.termType = '"+ TermType.Unknown.getKey() +"' " +
- " WHERE voc.termType IS NULL";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = "UPDATE TermVocabulary voc " + " SET voc.termType = '"
+ + TermType.Unknown.getKey() + "' "
+ + " WHERE voc.termType IS NULL";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
}
- private void updateTermTypeForVocabularies(List<ISchemaUpdaterStep> stepList, TermType termType) {
- String stepName = "Updater vocabulary termType for " + termType.toString();
- String query = "UPDATE TermVocabulary voc " +
- " SET voc.termType = '" + termType.getKey() + "' " +
- " WHERE Exists (SELECT * FROM DefinedTermBase dtb WHERE dtb.termType = '" + termType.getKey() + "' AND dtb.vocabulary_id = voc.id)";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing("TermVocabulary"); //AUD not fully correct as subselect should also work on AUD, good enough for our purposes
+ private void updateTermTypeForVocabularies(
+ List<ISchemaUpdaterStep> stepList, TermType termType) {
+ String stepName = "Updater vocabulary termType for "
+ + termType.toString();
+ String query = "UPDATE TermVocabulary voc "
+ + " SET voc.termType = '"
+ + termType.getKey()
+ + "' "
+ + " WHERE Exists (SELECT * FROM DefinedTermBase dtb WHERE dtb.termType = '"
+ + termType.getKey() + "' AND dtb.vocabulary_id = voc.id)";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ "TermVocabulary"); // AUD not fully correct as subselect
+ // should also work on AUD, good
+ // enough for our purposes
stepList.add(step);
}
private void updateTermTypesForTerms(List<ISchemaUpdaterStep> stepList) {
String stepName = "Update termType for NamedAreas";
String tableName = "DefinedTermBase";
-
- //NamedArea
- String query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NamedArea.getKey() + "' " +
- " WHERE DTYPE = '" + NamedArea.class.getSimpleName() + "' OR DTYPE = 'TdwgArea' OR DTYPE = '"+ Country.class.getSimpleName() + "' OR DTYPE = 'Continent' ";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //Lanugage
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Language.getKey() + "' " +
- " WHERE DTYPE = '" + Language.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+
+ // NamedArea
+ String query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NamedArea.getKey() + "' " + " WHERE DTYPE = '"
+ + NamedArea.class.getSimpleName()
+ + "' OR DTYPE = 'TdwgArea' OR DTYPE = '"
+ + Country.class.getSimpleName() + "' OR DTYPE = 'Continent' ";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName);
+ stepList.add(step);
+
+ // Lanugage
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Language.getKey() + "' " + " WHERE DTYPE = '"
+ + Language.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //RANK
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Rank.getKey() + "' " +
- " WHERE DTYPE = '" + Rank.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // RANK
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Rank.getKey() + "' " + " WHERE DTYPE = '"
+ + Rank.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //Feature
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Feature.getKey() + "' " +
- " WHERE DTYPE = '" + Feature.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+
+ // Feature
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Feature.getKey() + "' " + " WHERE DTYPE = '"
+ + Feature.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //AnnotationType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.AnnotationType.getKey() + "' " +
- " WHERE DTYPE = '" + AnnotationType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // AnnotationType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.AnnotationType.getKey() + "' " + " WHERE DTYPE = '"
+ + AnnotationType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //MarkerType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.MarkerType.getKey() + "' " +
- " WHERE DTYPE = '" + MarkerType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+
+ // MarkerType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.MarkerType.getKey() + "' " + " WHERE DTYPE = '"
+ + MarkerType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //ExtensionType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.ExtensionType.getKey() + "' " +
- " WHERE DTYPE = '" + ExtensionType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // ExtensionType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.ExtensionType.getKey() + "' " + " WHERE DTYPE = '"
+ + ExtensionType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //DerivationEventType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.DerivationEventType.getKey() + "' " +
- " WHERE DTYPE = '" + DerivationEventType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+
+ // DerivationEventType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.DerivationEventType.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + DerivationEventType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //PresenceAbsenceTerm
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.PresenceAbsenceTerm.getKey() + "' " +
- " WHERE DTYPE = 'PresenceTerm' OR DTYPE = 'AbsenceTerm'";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // PresenceAbsenceTerm
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.PresenceAbsenceTerm.getKey() + "' "
+ + " WHERE DTYPE = 'PresenceTerm' OR DTYPE = 'AbsenceTerm'";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //NomenclaturalStatusType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NomenclaturalStatusType.getKey() + "' " +
- " WHERE DTYPE = '" + NomenclaturalStatusType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // NomenclaturalStatusType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NomenclaturalStatusType.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + NomenclaturalStatusType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //NameRelationshipType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NameRelationshipType.getKey() + "' " +
- " WHERE DTYPE = '" + NameRelationshipType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // NameRelationshipType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NameRelationshipType.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + NameRelationshipType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //HybridRelationshipType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.HybridRelationshipType.getKey() + "' " +
- " WHERE DTYPE = '" + HybridRelationshipType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // HybridRelationshipType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.HybridRelationshipType.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + HybridRelationshipType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //SynonymRelationshipType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.SynonymRelationshipType.getKey() + "' " +
- " WHERE DTYPE = '" + SynonymRelationshipType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // SynonymRelationshipType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.SynonymRelationshipType.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + SynonymRelationshipType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //TaxonRelationshipType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.TaxonRelationshipType.getKey() + "' " +
- " WHERE DTYPE = '" + TaxonRelationshipType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // TaxonRelationshipType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.TaxonRelationshipType.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + TaxonRelationshipType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //NameTypeDesignationStatus
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NameTypeDesignationStatus.getKey() + "' " +
- " WHERE DTYPE = '" + NameTypeDesignationStatus.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // NameTypeDesignationStatus
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NameTypeDesignationStatus.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + NameTypeDesignationStatus.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //SpecimenTypeDesignationStatus
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.SpecimenTypeDesignationStatus.getKey() + "' " +
- " WHERE DTYPE = '" + SpecimenTypeDesignationStatus.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // SpecimenTypeDesignationStatus
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.SpecimenTypeDesignationStatus.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + SpecimenTypeDesignationStatus.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //InstitutionType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.InstitutionType.getKey() + "' " +
- " WHERE DTYPE = 'InstitutionType' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // InstitutionType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.InstitutionType.getKey() + "' "
+ + " WHERE DTYPE = 'InstitutionType' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //NamedAreaType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NamedAreaType.getKey() + "' " +
- " WHERE DTYPE = '" + NamedAreaType.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // NamedAreaType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NamedAreaType.getKey() + "' " + " WHERE DTYPE = '"
+ + NamedAreaType.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //NamedAreaLevel
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NamedAreaLevel.getKey() + "' " +
- " WHERE DTYPE = '" + NamedAreaLevel.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // NamedAreaLevel
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NamedAreaLevel.getKey() + "' " + " WHERE DTYPE = '"
+ + NamedAreaLevel.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //RightsType
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.RightsType.getKey() + "' " +
- " WHERE DTYPE = 'RightsType' OR DTYPE = 'RightsTerm' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // RightsType
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.RightsType.getKey() + "' "
+ + " WHERE DTYPE = 'RightsType' OR DTYPE = 'RightsTerm' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //MeasurementUnit
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.MeasurementUnit.getKey() + "' " +
- " WHERE DTYPE = '" + MeasurementUnit.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // MeasurementUnit
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.MeasurementUnit.getKey() + "' " + " WHERE DTYPE = '"
+ + MeasurementUnit.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //StatisticalMeasure
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.StatisticalMeasure.getKey() + "' " +
- " WHERE DTYPE = '" + StatisticalMeasure.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // StatisticalMeasure
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.StatisticalMeasure.getKey() + "' "
+ + " WHERE DTYPE = '" + StatisticalMeasure.class.getSimpleName()
+ + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //PreservationMethod
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Method.getKey() + "' " +
- " WHERE DTYPE = '" + PreservationMethod.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // PreservationMethod
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Method.getKey() + "' " + " WHERE DTYPE = '"
+ + PreservationMethod.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //Modifier
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Modifier.getKey() + "' " +
- " WHERE DTYPE = 'Modifier' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // Modifier
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Modifier.getKey() + "' "
+ + " WHERE DTYPE = 'Modifier' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //Scope
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Scope.getKey() + "' " +
- " WHERE DTYPE = 'Scope' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // Scope
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Scope.getKey() + "' " + " WHERE DTYPE = 'Scope' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //Stage
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Stage.getKey() + "' " +
- " WHERE DTYPE = 'Stage' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // Stage
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Stage.getKey() + "' " + " WHERE DTYPE = 'Stage' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //Sex
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.Sex.getKey() + "' " +
- " WHERE DTYPE = 'Sex' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // Sex
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.Sex.getKey() + "' " + " WHERE DTYPE = 'Sex' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //ReferenceSystem
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.ReferenceSystem.getKey() + "' " +
- " WHERE DTYPE = '" + ReferenceSystem.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // ReferenceSystem
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.ReferenceSystem.getKey() + "' " + " WHERE DTYPE = '"
+ + ReferenceSystem.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //State
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.State.getKey() + "' " +
- " WHERE DTYPE = '" + State.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // State
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.State.getKey() + "' " + " WHERE DTYPE = '"
+ + State.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //NaturalLanguageTerm
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.NaturalLanguageTerm.getKey() + "' " +
- " WHERE DTYPE = '" + NaturalLanguageTerm.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // NaturalLanguageTerm
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.NaturalLanguageTerm.getKey() + "' "
+ + " WHERE DTYPE = '"
+ + NaturalLanguageTerm.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //TextFormat
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.TextFormat.getKey() + "' " +
- " WHERE DTYPE = '" + TextFormat.class.getSimpleName() + "' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // TextFormat
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.TextFormat.getKey() + "' " + " WHERE DTYPE = '"
+ + TextFormat.class.getSimpleName() + "' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
- //DeterminationModifier
- query = " UPDATE DefinedTermBase " +
- " SET termType = '" + TermType.DeterminationModifier.getKey() + "' " +
- " WHERE DTYPE = 'DeterminationModifier' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ // DeterminationModifier
+ query = " UPDATE DefinedTermBase " + " SET termType = '"
+ + TermType.DeterminationModifier.getKey() + "' "
+ + " WHERE DTYPE = 'DeterminationModifier' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
}
/**
*/
private void updateDtypeOfDefinedTerms(List<ISchemaUpdaterStep> stepList) {
String tableName = "DefinedTermBase";
-
- //update DTYPE for institution type and modifiers (Stage, Scope, Sex, DeterminationModifier, Modifier) -> DefinedTerm
+
+ // update DTYPE for institution type and modifiers (Stage, Scope, Sex,
+ // DeterminationModifier, Modifier) -> DefinedTerm
String stepName = "Update DTYPE for TDWG Areas";
- String query = " UPDATE DefinedTermBase " +
- " SET DTYPE = 'DefinedTerm' " +
- " WHERE DTYPE = 'Stage' OR DTYPE = 'Scope' OR DTYPE = 'Sex' OR DTYPE = 'DeterminationModifier' " +
- " OR DTYPE = 'Modifier' OR DTYPE = 'InstitutionType' ";
- ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
-
- //update DTYPE for TDWG Areas and Continents -> NamedArea
+ String query = " UPDATE DefinedTermBase "
+ + " SET DTYPE = 'DefinedTerm' "
+ + " WHERE DTYPE = 'Stage' OR DTYPE = 'Scope' OR DTYPE = 'Sex' OR DTYPE = 'DeterminationModifier' "
+ + " OR DTYPE = 'Modifier' OR DTYPE = 'InstitutionType' ";
+ ISchemaUpdaterStep step = SimpleSchemaUpdaterStep
+ .NewNonAuditedInstance(stepName, query).setDefaultAuditing(
+ tableName);
+ stepList.add(step);
+
+ // update DTYPE for TDWG Areas and Continents -> NamedArea
stepName = "Update DTYPE for TDWG Areas and Continents";
- query = " UPDATE DefinedTermBase " +
- " SET DTYPE = 'NamedArea' " +
- " WHERE DTYPE = 'TdwgArea' OR DTYPE = 'Continent' ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = " UPDATE DefinedTermBase " + " SET DTYPE = 'NamedArea' "
+ + " WHERE DTYPE = 'TdwgArea' OR DTYPE = 'Continent' ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
+
}
/**
* @param stepList
*/
private void changeUriType(List<ISchemaUpdaterStep> stepList) {
- //#3345
+ // #3345
String stepName;
String tableName;
ISchemaUpdaterStep step;
String columnName;
-
+
stepName = "Update uri to clob for DefinedTermBase";
tableName = "DefinedTermBase";
columnName = "uri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update uri to clob for TermVocabulary";
tableName = "TermVocabulary";
columnName = "uri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //TODO are uri and termsourceuri needed ???
+
+ // TODO are uri and termsourceuri needed ???
stepName = "Update termsourceuri to clob for TermVocabulary";
tableName = "TermVocabulary";
columnName = "termsourceuri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update uri to clob for Reference";
tableName = "Reference";
columnName = "uri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
-
+
stepName = "Update uri to clob for Rights";
tableName = "Rights";
columnName = "uri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
stepName = "Update uri to clob for MediaRepresentationPart";
tableName = "MediaRepresentationPart";
columnName = "uri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //TODO still needed??
+
+ // TODO still needed??
stepName = "Update uri to clob for FeatureTree";
tableName = "FeatureTree";
columnName = "uri";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //Annotation.linkbackUri (change from URL to URI)
+
+ // Annotation.linkbackUri (change from URL to URI)
stepName = "Update url to uri (->clob) for Annotation.linkbackUri";
tableName = "Annotation";
columnName = "linkbackUrl";
- step = ColumnTypeChanger.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName,
+ columnName, INCLUDE_AUDIT);
stepList.add(step);
}
String tableName;
ISchemaUpdaterStep step;
String columnName;
- //start #3312
+ // start #3312
stepName = "Create time period start column in description element base";
tableName = "DescriptionElementBase";
columnName = "timeperiod_start";
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
- //end #3312
+ // end #3312
stepName = "Create time period end column in description element base";
tableName = "DescriptionElementBase";
columnName = "timeperiod_end";
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
- //freetext #3312
+ // freetext #3312
stepName = "Create time period freetext column in description element base";
tableName = "DescriptionElementBase";
columnName = "timeperiod_freetext";
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
+
return;
}
private void updateElevationMax(List<ISchemaUpdaterStep> stepList) {
- //create column
+ // create column
String stepName = "Create absoluteElevationMax column";
String tableName = "GatheringEvent";
String columnName = "absoluteElevationMax";
- ISchemaUpdaterStep step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false, null);
+ ISchemaUpdaterStep step = ColumnAdder.NewIntegerInstance(stepName,
+ tableName, columnName, INCLUDE_AUDIT, false, null);
stepList.add(step);
-
+
String audTableName = "GatheringEvent";
- //update max
+ // update max
stepName = "Update gathering elevation max";
- //all audits to unknown type
- String query = " UPDATE GatheringEvent ge " +
- " SET ge.absoluteElevationMax = ge.absoluteElevation + ge.absoluteElevationError, " +
- " ge.absoluteElevation = ge.absoluteElevation - ge.absoluteElevationError" +
- " WHERE ge.absoluteElevationError is not null ";
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(audTableName);
- stepList.add(step);
- //TODO same for AUD
-
- //remove error column
+ // all audits to unknown type
+ String query = " UPDATE GatheringEvent ge "
+ + " SET ge.absoluteElevationMax = ge.absoluteElevation + ge.absoluteElevationError, "
+ + " ge.absoluteElevation = ge.absoluteElevation - ge.absoluteElevationError"
+ + " WHERE ge.absoluteElevationError is not null ";
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(audTableName);
+ stepList.add(step);
+ // TODO same for AUD
+
+ // remove error column
stepName = "Remove elevationErrorRadius column";
tableName = "GatheringEvent";
columnName = "absoluteElevationError";
- step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ step = ColumnRemover.NewInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT);
stepList.add(step);
-
- //create column absoluteElevationText
+
+ // create column absoluteElevationText
stepName = "Create absoluteElevationText column";
tableName = "GatheringEvent";
columnName = "absoluteElevationText";
int size = 30;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, size, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ size, INCLUDE_AUDIT);
stepList.add(step);
-
- //retype distanceToGround
+
+ // retype distanceToGround
stepName = "Rname distanceToGround column";
tableName = "GatheringEvent";
String strOldColumnName = "distanceToGround";
- step = ColumnTypeChanger.NewInt2DoubleInstance(stepName, tableName, strOldColumnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewInt2DoubleInstance(stepName, tableName,
+ strOldColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //create column distanceToGroundMax
+
+ // create column distanceToGroundMax
stepName = "Create distanceToGroundMax column";
tableName = "GatheringEvent";
columnName = "distanceToGroundMax";
- step = ColumnAdder.NewDoubleInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ step = ColumnAdder.NewDoubleInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false);
stepList.add(step);
-
-
- //create column distanceToGroundText
+
+ // create column distanceToGroundText
stepName = "Create distanceToGroundText column";
tableName = "GatheringEvent";
columnName = "distanceToGroundText";
size = 30;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, size, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ size, INCLUDE_AUDIT);
stepList.add(step);
-
- //retype distanceToGround
+
+ // retype distanceToGround
stepName = "Rname distanceToWaterSurface column";
tableName = "GatheringEvent";
strOldColumnName = "distanceToWaterSurface";
- step = ColumnTypeChanger.NewInt2DoubleInstance(stepName, tableName, strOldColumnName, INCLUDE_AUDIT);
+ step = ColumnTypeChanger.NewInt2DoubleInstance(stepName, tableName,
+ strOldColumnName, INCLUDE_AUDIT);
stepList.add(step);
-
- //create column distanceToWaterSurface
+
+ // create column distanceToWaterSurface
stepName = "Create distanceToWaterSurfaceMax column";
tableName = "GatheringEvent";
columnName = "distanceToWaterSurfaceMax";
- step = ColumnAdder.NewDoubleInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ step = ColumnAdder.NewDoubleInstance(stepName, tableName, columnName,
+ INCLUDE_AUDIT, false);
stepList.add(step);
-
-
- //create column distanceToGroundText
+
+ // create column distanceToGroundText
stepName = "Create distanceToWaterSurfaceText column";
tableName = "GatheringEvent";
columnName = "distanceToWaterSurfaceText";
size = 30;
- step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, size, INCLUDE_AUDIT);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName,
+ size, INCLUDE_AUDIT);
stepList.add(step);
}
String typeAttrName = "sourceType";
ISchemaUpdaterStep step;
String tableName = "OriginalSourceBase";
-
- //all data to unknown
+
+ // all data to unknown
stepName = "Update original source type column: set all to unknown";
- String query = String.format("UPDATE OriginalSourceBase " +
- " SET %s = '%s' ", typeAttrName, OriginalSourceType.Unknown.getKey());
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ String query = String.format("UPDATE OriginalSourceBase "
+ + " SET %s = '%s' ", typeAttrName,
+ OriginalSourceType.Unknown.getKey());
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
-
- //all IMPORTS recognized by idInSOurce and by missing nameInSource
+
+ // all IMPORTS recognized by idInSOurce and by missing nameInSource
stepName = "Update original source type column: set to 'import' where possible";
- query = String.format("UPDATE OriginalSourceBase " +
- " SET %s = '%s' " +
- " WHERE " +
- "((idInSource IS NOT NULL) OR (idNamespace IS NOT NULL)) AND " +
- "( nameUsedInSource_id IS NULL AND originalNameString IS NULL ) ", typeAttrName, OriginalSourceType.Import.getKey());
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
- stepList.add(step);
-
- //all PRIMARY TAXONOMIC SOURCES recognized by missing idInSource and namespace and by existing citation
+ query = String
+ .format("UPDATE OriginalSourceBase "
+ + " SET %s = '%s' "
+ + " WHERE "
+ + "((idInSource IS NOT NULL) OR (idNamespace IS NOT NULL)) AND "
+ + "( nameUsedInSource_id IS NULL AND originalNameString IS NULL ) ",
+ typeAttrName, OriginalSourceType.Import.getKey());
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
+ stepList.add(step);
+
+ // all PRIMARY TAXONOMIC SOURCES recognized by missing idInSource and
+ // namespace and by existing citation
stepName = "Update original source type column: set to 'primary taxonomic source' where possible";
- query = String.format("UPDATE OriginalSourceBase SET %s = '%s' WHERE " +
- "(idInSource IS NULL AND idNamespace IS NULL) AND " +
- "( citation_id IS NOT NULL ) ", typeAttrName, OriginalSourceType.PrimaryTaxonomicSource.getKey());
- step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query).setDefaultAuditing(tableName);
+ query = String.format("UPDATE OriginalSourceBase SET %s = '%s' WHERE "
+ + "(idInSource IS NULL AND idNamespace IS NULL) AND "
+ + "( citation_id IS NOT NULL ) ", typeAttrName,
+ OriginalSourceType.PrimaryTaxonomicSource.getKey());
+ step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query)
+ .setDefaultAuditing(tableName);
stepList.add(step);
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getNextUpdater()
*/
@Override
return null;
}
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getPreviousUpdater()
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.cdm.database.update.SchemaUpdaterBase#getPreviousUpdater()
*/
@Override
public ISchemaUpdater getPreviousUpdater() {
BGBM BDI Projects / cdmlib.git / commitdiff