--- /dev/null
+// $Id$\r
+/**\r
+* Copyright (C) 2009 EDIT\r
+* European Distributed Institute of Taxonomy \r
+* http://www.e-taxonomy.eu\r
+* \r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.database.update;\r
+\r
+import java.sql.SQLException;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;\r
+import eu.etaxonomy.cdm.database.DatabaseTypeEnum;\r
+import eu.etaxonomy.cdm.database.ICdmDataSource;\r
+\r
+/**\r
+ * @author a.mueller\r
+ * @date 16.09.2010\r
+ *\r
+ */\r
+public class ColumnTypeChanger extends SchemaUpdaterStepBase<ColumnTypeChanger> implements ISchemaUpdaterStep {\r
+ private static final Logger logger = Logger.getLogger(ColumnTypeChanger.class);\r
+ \r
+ private String tableName;\r
+ private String newColumnName;\r
+ private String oldColumnName;\r
+ private String newColumnType;\r
+ private boolean includeAudTable;\r
+ private Object defaultValue;\r
+ private boolean isNotNull;\r
+ private String referencedTable;\r
+\r
+ \r
+ public static final ColumnTypeChanger NewClobInstance(String stepName, String tableName, String oldColumnName, String newColumnName, boolean includeAudTable){\r
+ return new ColumnTypeChanger(stepName, tableName, oldColumnName, newColumnName, "clob", includeAudTable, null, false, null);\r
+ }\r
+ \r
+ public static final ColumnTypeChanger NewInt2DoubleInstance(String stepName, String tableName, String oldColumnName, String newColumnName, boolean includeAudTable){\r
+ return new ColumnTypeChanger(stepName, tableName, oldColumnName, newColumnName, "double", includeAudTable, null, false, null);\r
+ }\r
+ \r
+ protected ColumnTypeChanger(String stepName, String tableName, String oldColumnName, String newColumnName, String newColumnType, boolean includeAudTable, Object defaultValue, boolean notNull, String referencedTable) {\r
+ super(stepName);\r
+ this.tableName = tableName;\r
+ this.newColumnName = newColumnName;\r
+ this.newColumnType = newColumnType;\r
+ this.oldColumnName =oldColumnName;\r
+ this.includeAudTable = includeAudTable;\r
+ this.defaultValue = defaultValue;\r
+ this.isNotNull = notNull;\r
+ this.referencedTable = referencedTable;\r
+ }\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.database.update.SchemaUpdaterStepBase#invoke(eu.etaxonomy.cdm.database.ICdmDataSource, eu.etaxonomy.cdm.common.IProgressMonitor)\r
+ */\r
+ @Override\r
+ public Integer invoke(ICdmDataSource datasource, IProgressMonitor monitor) throws SQLException {\r
+ boolean result = true;\r
+ result &= changeColumn(tableName, datasource, monitor);\r
+ if (includeAudTable){\r
+ String aud = "_AUD";\r
+ result &= changeColumn(tableName + aud, datasource, monitor);\r
+ }\r
+ return (result == true )? 0 : null;\r
+ }\r
+\r
+ private boolean changeColumn(String tableName, ICdmDataSource datasource, IProgressMonitor monitor) {\r
+ boolean result = true;\r
+ try {\r
+ String updateQuery = getUpdateQueryString(tableName, datasource, monitor);\r
+ try {\r
+ datasource.executeUpdate(updateQuery);\r
+ } catch (SQLException e) {\r
+ logger.error(e);\r
+ result = false;\r
+ }\r
+ \r
+ if (defaultValue instanceof Boolean){\r
+ updateQuery = "UPDATE @tableName SET @columnName = " + (defaultValue == null ? "null" : getBoolean((Boolean) defaultValue, datasource));\r
+ updateQuery = updateQuery.replace("@tableName", tableName);\r
+ updateQuery = updateQuery.replace("@columnName", newColumnName);\r
+ try {\r
+ datasource.executeUpdate(updateQuery);\r
+ } catch (SQLException e) {\r
+ logger.error(e);\r
+ result = false;\r
+ }\r
+ }\r
+ if (referencedTable != null){\r
+ result &= TableCreator.makeForeignKey(tableName, datasource, newColumnName, referencedTable);\r
+ }\r
+ \r
+ return result;\r
+ } catch ( DatabaseTypeNotSupportedException e) {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ public String getUpdateQueryString(String tableName, ICdmDataSource datasource, IProgressMonitor monitor) throws DatabaseTypeNotSupportedException {\r
+ String updateQuery;\r
+ DatabaseTypeEnum type = datasource.getDatabaseType();\r
+ String databaseColumnType = getDatabaseColumnType(datasource, this.newColumnType);\r
+\r
+ if (type.equals(DatabaseTypeEnum.SqlServer2005)){\r
+ //MySQL allows both syntaxes\r
+ updateQuery = "ALTER TABLE @tableName ALTER COLUMN @columnName @columnType";\r
+ }else if (type.equals(DatabaseTypeEnum.H2)){\r
+ updateQuery = "ALTER TABLE @tableName ALTER COLUMN @columnName @columnType";\r
+ }else if (type.equals(DatabaseTypeEnum.PostgreSQL)){\r
+ updateQuery = "ALTER TABLE @tableName ALTER COLUMN @columnName TYPE @columnType";\r
+ }else if (type.equals(DatabaseTypeEnum.MySQL)){\r
+ updateQuery = "ALTER TABLE @tableName MODIFY COLUMN @columnName @columnType";\r
+ }else{\r
+ updateQuery = null;\r
+ String warning = "Update step '" + this.getStepName() + "' is not supported by " + type.getName();\r
+ monitor.warning(warning);\r
+ throw new DatabaseTypeNotSupportedException(warning);\r
+ }\r
+ if (isNotNull){\r
+ updateQuery += " NOT NULL";\r
+ }\r
+ updateQuery = updateQuery.replace("@tableName", tableName);\r
+ updateQuery = updateQuery.replace("@columnName", newColumnName);\r
+ updateQuery = updateQuery.replace("@columnType", databaseColumnType);\r
+// updateQuery = updateQuery.replace("@addSeparator", getAddColumnSeperator(datasource));\r
+ \r
+ return updateQuery;\r
+ }\r
+\r
+ private String getDatabaseColumnType(ICdmDataSource datasource, String columnType) {\r
+ return ColumnAdder.getDatabaseColumnType(datasource, columnType);\r
+ }\r
+ \r
+ public String getReferencedTable() {\r
+ return referencedTable;\r
+ }\r
+\r
+ public String getNewColumnName() {\r
+ return newColumnName;\r
+ }\r
+\r
+}\r
import com.sun.tools.xjc.reader.gbind.Sequence;
import eu.etaxonomy.cdm.database.update.ColumnAdder;
+import eu.etaxonomy.cdm.database.update.ColumnNameChanger;
import eu.etaxonomy.cdm.database.update.ColumnRemover;
+import eu.etaxonomy.cdm.database.update.ColumnTypeChanger;
import eu.etaxonomy.cdm.database.update.ISchemaUpdater;
import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
+import eu.etaxonomy.cdm.database.update.MnTableCreator;
import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;
import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;
import eu.etaxonomy.cdm.database.update.TableCreator;
*/
public class SchemaUpdater_31_33 extends SchemaUpdaterBase {
-
- @SuppressWarnings("unused")
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 = "3.3.0.0.201308010000";
stepName = "Create original source type column";
tableName = "OriginalSourceBase";
String columnName = "sourceType";
- //TODO NOT NULL unclear
- step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, true, null);
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 4, INCLUDE_AUDIT);
+ ((ColumnAdder)step).setNotNull(true);
stepList.add(step);
//TODO ?? update original source type
//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);
+ stepList.add(step);
+
+
//TODO update termType for DefinedTerms and TermVocabulary, no type must be null
//TODO add column for DistanceToWaterSurfaceMax/Text und DistanceToGroundMax/Text
- //TODO update datatype of sequence.sequence => CLOB (keeping data not necessary #3325)
- //NOTE: column 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);
- //TODO update datatype->CLOB for URIs. (DefinedTerms, TermVocabulary, Reference
- //Rights, MediaRepresentationPart ) #3345
//update Sicilia -> Sicily
//#3540
stepList.add(step);
//TODO 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);
+ stepList.add(step);
+
+ stepName = "Add abbrevTitleCache to Reference";
+ tableName = "Reference";
+ columnName = "abbrevTitleCache";
+ length = 1023;
+ 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);
+ stepList.add(step);
+
+ //add doi to reference
+ stepName = "Add doi to Reference";
+ tableName = "Reference";
+ columnName = "doi";
+ length = 255;
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ stepList.add(step);
//add start number to PolytomousKey
step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, defaultValue, true);
stepList.add(step);
- //TODO add specimenOrObservation basis of record to SpecimenOrObservationBase
+ //add recordBasis to specimenOrObservationBase
+ stepName = "Add recordBasis to SpecimenOrObservationBase";
+ tableName = "SpecimenOrObservationBase";
+ columnName = "recordBasis";
+ length = 4;
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ stepList.add(step);
+
+
//TODO update specimenOrObservationBase DTYPE with DefinedTerm where necessary
//TODO update length of all title caches and full title cache in names
//https://dev.e-taxonomy.eu/trac/ticket/1592
- //TODO 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";
+ String newColumnName = "stateData_id";
+ step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
//TODO add sortIndex column to TaxonNode and fill with values (compare with FeatureNode filling, however, this
// had a bad performance
//specimen descriptions #3571
//TODO add column DescriptionBase.Specimen_ID #3571
stepName = "Add specimen_id column to DescriptionBase";
- tableName = "SpecimenOrObservationBase";
+ tableName = "DescriptionBase";
columnName = "specimen_id";
boolean notNull = false;
String referencedTable = "SpecimenOrObservationBase";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
- //TODO create table CdmPreferences #3555
+ //create table CdmPreferences #3555
+ stepName = "Create table 'CdmPreferences'";
+ tableName = "CdmPreferences";
+ TableCreator stepPref = TableCreator.NewInstance(stepName, tableName,
+ new String[]{"key_subject", "key_predicate","value"}, //colNames
+ new String[]{"string_100", "string_200","string_1023",}, // columnTypes
+ new String[]{null, "DefinedTermBase",null}, //referencedTables
+ ! INCLUDE_AUDIT, false);
+ stepPref.setPrimaryKeyParams("key_subject, key_predicate", null);
+ stepList.add(stepPref);
+ //TODO length of key >= 1000
//TODO fill CdmPreferences with default values
//TODO add Marker vocabulary and terms #3591 => TermUpdater
- //SpecimenOrObservationBase_Media #3597
+ //SpecimenOrObservationBase_Media #3597
stepName = "Remove table SpecimenOrObservationBase_Media";
tableName = "SpecimenOrObservationBase_Media";
step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT);
stepList.add(step);
+ //Amplification #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
+ INCLUDE_AUDIT);
+ stepList.add(step);
+ //MaterialAndMethod #3360
+ stepName = "Create table 'MaterialAndMethod'";
+ tableName = MaterialAndMethod.class.getSimpleName();
+ step = TableCreator.NewAnnotatableInstance(stepName, tableName,
+ new String[]{"DTYPE", "materialMethodTerm_id","materialMethodText"}, //colNames
+ new String[]{"string_255", "int","string_1000",}, // columnTypes
+ new String[]{null, "DefinedTermBase",null}, //referencedTables
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //Cloning #3360
+ stepName = "Create table 'Cloning'";
+ tableName = "Cloning";
+ String matMetName = MaterialAndMethod.class.getSimpleName();
+ step = TableCreator.NewEventInstance(stepName, tableName,
+ new String[]{"strain","method_id","forwardPrimer_id","reversePrimer_id"}, //colNames
+ new String[]{"string_255", "int","int","int"}, // columnTypes
+ new String[]{null, matMetName,"Primer","Primer"}, //referencedTables
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+
+ //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",matMetName, matMetName, "Media", null, null, null, null, null, null}, //referencedTables
+ INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //SingleRead #3360
+ stepName = "Create table 'SingleRead'";
+ tableName = "SingleRead";
+ step = TableCreator.NewEventInstance(stepName, tableName,
+ new String[]{"amplification_id","materialAndMethod_id","primer_id","pherogram_id","direction","sequence_length"}, //colNames
+ new String[]{"int","int","int","int","int","int"}, // columnTypes
+ new String[]{"Amplification",matMetName, "Primer","Media", null, null}, //referencedTables
+ INCLUDE_AUDIT);
+ //TODO length sequence_string
+ stepList.add(step);
+
+ //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";
+ tableName = "Sequence";
+ columnName = "barcodeSequencePart_length";
+ defaultValue = null;
+ step = ColumnAdder.NewIntegerInstance(stepName, tableName, columnName, INCLUDE_AUDIT, defaultValue, false);
+ stepList.add(step);
+
+ //sequence - barcode #3360
+ stepName= "Add barcodesequencepart_string to sequence";
+ tableName = "Sequence";
+ columnName = "barcodeSequencePart_string";
+ step = ColumnAdder.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //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);
+ stepList.add(step);
+
+ //sequence - consensussequence_string #3360
+ stepName= "Add consensusSequence_string to sequence";
+ tableName = "Sequence";
+ columnName = "consensusSequence_string";
+ step = ColumnAdder.NewClobInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //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);
+ stepList.add(step);
+
+ //sequence - boldprocessid #3360
+ stepName= "Add boldprocessId to sequence";
+ tableName = "Sequence";
+ columnName = "boldProcessId";
+ length = 20;
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //sequence - boldprocessid #3360
+ stepName= "Add geneticAccessionNumber to sequence";
+ tableName = "Sequence";
+ columnName = "geneticAccessionNumber";
+ length = 20;
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //sequence - haplotype #3360
+ stepName= "Add haplotype to sequence";
+ tableName = "Sequence";
+ columnName = "haplotype";
+ length = 100;
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, length, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //sequence - isBarcode #3360
+ stepName= "Add isBarcode to sequence";
+ tableName = "Sequence";
+ columnName = "isBarcode";
+ step = ColumnAdder.NewBooleanInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ stepList.add(step);
+
+ //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);
+ stepList.add(step);
+
+ //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);
+ stepList.add(step);
return stepList;
}
+ /**
+ * @param stepList
+ */
+ private void changeUriType(List<ISchemaUpdaterStep> stepList) {
+ String stepName;
+ String tableName;
+ ISchemaUpdaterStep step;
+ stepName = "Update uri to clob for DefinedTermBase";
+ tableName = "DefinedTermBase";
+ String oldColumnName = "uri";
+ String newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ stepName = "Update uri to clob for TermVocabulary";
+ tableName = "TermVocabulary";
+ oldColumnName = "uri";
+ newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //TODO are uri and termsourceuri needed ???
+ stepName = "Update termsourceuri to clob for TermVocabulary";
+ tableName = "TermVocabulary";
+ oldColumnName = "termsourceuri";
+ newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ stepName = "Update uri to clob for Reference";
+ tableName = "Reference";
+ oldColumnName = "uri";
+ newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ stepName = "Update uri to clob for Rights";
+ tableName = "Rights";
+ oldColumnName = "uri";
+ newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ stepName = "Update uri to clob for MediaRepresentationPart";
+ tableName = "MediaRepresentationPart";
+ oldColumnName = "uri";
+ newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //TODO still needed??
+ stepName = "Update uri to clob for FeatureTree";
+ tableName = "FeatureTree";
+ oldColumnName = "uri";
+ newColumnName = oldColumnName;
+ step = ColumnTypeChanger.NewClobInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ }
+
/**
* @param stepList
* @return
step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
stepList.add(step);
- //Amplification #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
- INCLUDE_AUDIT);
- stepList.add(step);
-
- //MaterialAndMethod #3360
- stepName = "Create table 'MaterialAndMethod'";
- tableName = MaterialAndMethod.class.getSimpleName();
- step = TableCreator.NewAnnotatableInstance(stepName, tableName,
- new String[]{"materialMethodTerm_id","materialMethodText"}, //colNames
- new String[]{"int","string_1000",}, // columnTypes
- new String[]{"DefinedTermBase",null}, //referencedTables
- INCLUDE_AUDIT);
- stepList.add(step);
-
- //Amplification #3360
- stepName = "Create table 'Amplification'";
- tableName = "Amplification";
- String matMetName = MaterialAndMethod.class.getSimpleName();
- step = TableCreator.NewEventInstance(stepName, tableName,
- new String[]{"dnaSample_id","dnaMarker_id","forwardPrimer_id","reversePrimer_id","purification_id","cloning_id"}, //colNames
- new String[]{"int","int","int","int","int","int"}, // columnTypes
- new String[]{"SpecimenOrObservationBase","DefinedTermBase","Primer","Primer",matMetName, matMetName}, //referencedTables
- INCLUDE_AUDIT);
- stepList.add(step);
-
- //Amplification #3360
- stepName = "Create table 'SingleRead'";
- tableName = "SingleReadSingleRead";
- step = TableCreator.NewEventInstance(stepName, tableName,
- new String[]{"amplification_id","materialAndMethod_id","primer_id","pherogram_id","direction","sequenceString_length","sequenceString_sequence"}, //colNames
- new String[]{"int","int","int","int","int","int","string_1000"}, // columnTypes
- new String[]{"Amplification",matMetName, "Primer","Media", null, null}, //referencedTables
- INCLUDE_AUDIT);
- stepList.add(step);
-
-
return;
}
step = ColumnRemover.NewInstance(stepName, tableName, columnName, INCLUDE_AUDIT);
stepList.add(step);
+ //create column absoluteElevationText
+ stepName = "Create absoluteElevationText column";
+ tableName = "GatheringEvent";
+ columnName = "absoluteElevationText";
+ //TODO size
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //retype distanceToGround
+ stepName = "Rname distanceToGround column";
+ tableName = "GatheringEvent";
+ String strNewColumnName = "distanceToGround";
+ String strOldColumnName = "distanceToGround";
+ step = ColumnTypeChanger.NewInt2DoubleInstance(stepName, tableName, strOldColumnName, strNewColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //create column distanceToGroundMax
+ stepName = "Create distanceToGroundMax column";
+ tableName = "GatheringEvent";
+ columnName = "distanceToGroundMax";
+ step = ColumnAdder.NewDoubleInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ stepList.add(step);
+
+ //create column distanceToGroundText
+ stepName = "Create distanceToGroundText column";
+ tableName = "GatheringEvent";
+ columnName = "distanceToGroundText";
+ //TODO size
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //retype distanceToGround
+ stepName = "Rname distanceToWaterSurface column";
+ tableName = "GatheringEvent";
+ strNewColumnName = "distanceToWaterSurface";
+ strOldColumnName = "distanceToWaterSurface";
+ step = ColumnTypeChanger.NewInt2DoubleInstance(stepName, tableName, strOldColumnName, strNewColumnName, INCLUDE_AUDIT);
+ stepList.add(step);
+
+ //create column distanceToWaterSurface
+ stepName = "Create distanceToWaterSurfaceMax column";
+ tableName = "GatheringEvent";
+ columnName = "distanceToWaterSurfaceMax";
+ step = ColumnAdder.NewDoubleInstance(stepName, tableName, columnName, INCLUDE_AUDIT, false);
+ stepList.add(step);
+
+
+ //create column distanceToGroundText
+ stepName = "Create distanceToWaterSurfaceText column";
+ tableName = "GatheringEvent";
+ columnName = "distanceToWaterSurfaceText";
+ //TODO size
+ step = ColumnAdder.NewStringInstance(stepName, tableName, columnName, 255, INCLUDE_AUDIT);
+ stepList.add(step);
+
}
/**
BGBM BDI Projects / cdmlib.git / commitdiff