Package net.sf.basedb.core

Class MigrateRbaToDba

java.lang.Object

net.sf.basedb.core.MigrateRbaToDba

All Implemented Interfaces:

Work

public class MigrateRbaToDba
extends Object
implements Work

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MigrateRbaToDba.Itemlist
static class	MigrateRbaToDba.LineMapping
static class	MigrateRbaToDba.MigratedLogger	Used for adding log entries to the database if that is enabled.
static class	MigrateRbaToDba.Rba	Hold information a raw bioassay.
static class	MigrateRbaToDba.SubtypeMapping	Hold the mappings defined in the mapping file.

Field Summary

Fields

Modifier and Type	Field	Description
private final List<AnnotationBatcher.InsertBatcher>	allInsertBatchers
private final List<AnnotationBatcher.UpdateBatcher>	allUpdateBatchers
private final DbControl	dc
private final Dialect	dialect
private final LoggingInterceptor	logInterceptor
private final MigrateRbaToDba.SubtypeMapping	mapping
private final ProgressReporter	progress
private final StatelessSession	session

Constructor Summary

Constructors

Modifier	Constructor	Description
private	MigrateRbaToDba(DbControl dc, MigrateRbaToDba.SubtypeMapping mapping, ProgressReporter progress)

Method Summary

Modifier and Type	Method	Description
private AnnotationBatcher.InsertBatcher	createInsertBatcher(Connection c, String sql, int... types)
private AnnotationBatcher.UpdateBatcher	createUpdateBatcher(Connection c, String sql, int... types)
private void	enableAnnotationTypes(Connection connection, List<Integer> allAnnotationSets)	Make sure that the annotation types that are used by the migrated raw bioassays are enabled for derived bioassays.
private void	enableFileTypes(Connection connection, List<Integer> allFileSets)	Make sure that the data file types that are used by the migrated raw bioassays are enabled for derived bioassays.
void	execute(Connection connection)
private void	flush()	Flush all batchers
private void	linkItemValues(Connection connection, Map<Integer,Integer> rbaToDba)	Change raw bioassays that have been used as job parameters to the new derived bioassay.
static void	migrateAll(SessionControl sc, File cfg, boolean dryRun, ProgressReporter progress)
private void	updateItemLists(Connection connection, Map<Integer,Integer> rbaToDba)	Update item lists with raw bioassays to item lists with derived bioassays.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

dc

private final DbControl dc

logInterceptor

private final LoggingInterceptor logInterceptor

mapping

private final MigrateRbaToDba.SubtypeMapping mapping

progress

private final ProgressReporter progress

session

private final StatelessSession session

dialect

private final Dialect dialect

allInsertBatchers

private final List<AnnotationBatcher.InsertBatcher> allInsertBatchers

allUpdateBatchers

private final List<AnnotationBatcher.UpdateBatcher> allUpdateBatchers

Constructor Details

MigrateRbaToDba

private MigrateRbaToDba(DbControl dc,
 MigrateRbaToDba.SubtypeMapping mapping,
 ProgressReporter progress)

Method Details

migrateAll

public static void migrateAll(SessionControl sc,
 File cfg,
 boolean dryRun,
 ProgressReporter progress)
                       throws SQLException,
IOException

Throws:

SQLException

IOException

execute

public void execute(Connection connection)
             throws SQLException

Specified by:

execute in interface Work

Throws:

SQLException

enableAnnotationTypes

private void enableAnnotationTypes(Connection connection,
 List<Integer> allAnnotationSets)
                            throws SQLException

Make sure that the annotation types that are used by the migrated raw bioassays are enabled for derived bioassays.

Throws:

SQLException

enableFileTypes

private void enableFileTypes(Connection connection,
 List<Integer> allFileSets)
                      throws SQLException

Make sure that the data file types that are used by the migrated raw bioassays are enabled for derived bioassays.

Throws:

SQLException

linkItemValues

private void linkItemValues(Connection connection,
 Map<Integer,Integer> rbaToDba)
                     throws SQLException

Change raw bioassays that have been used as job parameters to the new derived bioassay. It would have been possible to do this per raw bioassay but it goes a lot faster if we can use the 'id' column in the update query.

Throws:

SQLException

updateItemLists

private void updateItemLists(Connection connection,
 Map<Integer,Integer> rbaToDba)
                      throws SQLException

Update item lists with raw bioassays to item lists with derived bioassays.

Throws:

SQLException

createInsertBatcher

private AnnotationBatcher.InsertBatcher createInsertBatcher(Connection c,
 String sql,
 int... types)
                                                     throws SQLException

Throws:

SQLException

createUpdateBatcher

private AnnotationBatcher.UpdateBatcher createUpdateBatcher(Connection c,
 String sql,
 int... types)
                                                     throws SQLException

Throws:

SQLException

flush

private void flush()

Flush all batchers