Package net.sf.basedb.core

Class PositionBatcher

java.lang.Object

net.sf.basedb.core.AbstractBatcher

net.sf.basedb.core.PositionBatcher

All Implemented Interfaces:

AutoCloseable, Batcher

public class PositionBatcher
extends AbstractBatcher

Batcher class for per-position data in the dynamic database. This batcher is used to insert data that is valid for all positions in a data cube.

Normally this means linking a position to a reporter.

Code example: Dynamic API - Creating a root bioassayset

Version:

2.0

Author:

Nicklas

See Also:

• BioAssaySet.getPositionBatcher()

Last modified

$Date: 2015-04-21 09:59:42 +0200 (ti, 21 apr 2015) $

Field Summary

Fields

Modifier and Type	Field	Description
private long	bytes	The number of bytes this batcher has added to the data cube and experiment.
private final long	bytesPerRow	The number of bytes used by a single row.
private final DataCube	dataCube	The datacube this batcher inserts data for.
private int	maxPosition	The maximum position number inserted by the batcher.
private PreparedStatement	positionSql	The statement that inserts the position/reporter link.
private String	positionSqlStatement	The SQL string for the positionSql statement.
private int	queuedInsertCount	The number of queued inserts.
private int	totalInsertCount	The total number of inserts done by this batcher.

Fields inherited from class net.sf.basedb.core.AbstractBatcher

debugSqlEnabled, logSql

Constructor Summary

Constructors

Constructor	Description
PositionBatcher(DbControl dc, DataCube dataCube)	Create a new position batcher for a data cube.

Method Summary

Modifier and Type	Method	Description
private String	buildInsertSelectSql(String selectSql)	Build the INSERT INTO ...
private void	buildPositionSql()	Builds the insert SQL statement.
void	flush()	Flush the batcher and send all remaining items in memory to the database.
void	insert(int position, ReporterData reporter)	Link a position to a reporter.
int	insert(AbstractSqlQuery query)	Insert position/reporter links using a query.
(package private) void	onBeforeClose()	Update bytes and max position on the datacube and close open SQL statements.

Methods inherited from class net.sf.basedb.core.AbstractBatcher

analyzeTable, close, getBatchSize, getDbControl, getSessionControl, isClosed, setBatchSize, setDbControl, updateLastAccess

Methods inherited from class java.lang.Object

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

Field Details

dataCube

private final DataCube dataCube

The datacube this batcher inserts data for.

queuedInsertCount

private int queuedInsertCount

The number of queued inserts. Used to check when a flush is needed.

totalInsertCount

private int totalInsertCount

The total number of inserts done by this batcher.

maxPosition

private int maxPosition

The maximum position number inserted by the batcher.

bytes

private long bytes

The number of bytes this batcher has added to the data cube and experiment.

bytesPerRow

private final long bytesPerRow

The number of bytes used by a single row.

positionSql

private PreparedStatement positionSql

The statement that inserts the position/reporter link.

INSERT INTO Dynamic#PerPosition (cube, position, reporter_id)
VALUES (cube, ?, ?)

positionSqlStatement

private String positionSqlStatement

The SQL string for the positionSql statement.

Constructor Details

PositionBatcher

PositionBatcher(DbControl dc,
 DataCube dataCube)

Create a new position batcher for a data cube. It is assumed that the calling code has checked that the cube is allowed to receive more data (ie. it hasn't been committed to the database).

Method Details

flush

public void flush()
           throws BaseException

Description copied from interface: Batcher

Flush the batcher and send all remaining items in memory to the database.

Throws:

BaseException - If there is an error

See Also:

• Batcher.close()

onBeforeClose

void onBeforeClose()
            throws BaseException

Update bytes and max position on the datacube and close open SQL statements.

Overrides:

onBeforeClose in class AbstractBatcher

Throws:

BaseException

insert

public void insert(int position,
 ReporterData reporter)
            throws BaseException

Link a position to a reporter.

Parameters:

position - The position coordinate

reporter - The reporter or null if no reporter is known

Throws:

BaseException - If there is an error

insert

public int insert(AbstractSqlQuery query)
           throws BaseException

Insert position/reporter links using a query. The query MUST select data in the following order: position, reporterId

Internally this method converts the query into a INSERT INTO ... SELECT ... query, making it very fast, since the data for each position doesn't have to be retreived, processed and then inserted one row at a time. It is possible to call this method multiple times with the same or different query.

Parameters:

query - The query that selects the data to be inserted

Returns:

int The number of rows inserted

Throws:

BaseException - If there is an error

buildPositionSql

private void buildPositionSql()
                       throws SQLException,
BaseException

Builds the insert SQL statement. Also creates the Dynamic#PerPosition table if it doesn't exists.

Throws:

SQLException

BaseException

See Also:

• BatchUtil.buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[])

buildInsertSelectSql

private String buildInsertSelectSql(String selectSql)
                             throws BaseException

Build the INSERT INTO ... SELECT ... statment. Also creates the Dynamic#PerPosition table if it doesn't exists.

Parameters:

selectSql - The SELECT part of the query

Throws:

BaseException

See Also:

• BatchUtil.buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String)