net.sf.basedb.core
Class MappingBatcher

java.lang.Object
  net.sf.basedb.core.AbstractBatcher
      net.sf.basedb.core.MappingBatcher

All Implemented Interfaces:

Batcher

public class MappingBatcher
extends AbstractBatcher

Batcher class for inserting parent mapping information in the dynamic database. This batcher is used to map data cube spots to their parent RawData.

Code example: Dynamic API - Creating a root bioassayset

Version:

2.0

Author:

Nicklas

See Also:

BioAssaySet.getMappingBatcher()

Last modified

$Date: 2009-06-23 11:56:00 +0200 (Tue, 23 Jun 2009) $

Field Summary

private long	bytes The number of bytes this batcher has added to the experiment.
private long	bytesPerRow The number of bytes used by a single row.
private DataCube	dataCube The datacube this batcher inserts data for.
private boolean	noRawMapping If the data cube has already received it's data and no raw data can be linked.
private int	queuedInsertCount The number of queued inserts.
private PreparedStatement	rawMappingSql The statement that inserts the spot/raw data link.
private String	rawMappingSqlStatement The SQL string for the rawMappingSql statement.
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

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

Method Summary

private String	buildInsertSelectSql(String selectSql) Build the INSERT INTO ...
private void	buildRawMappingSql() Builds the insert SQL statement.
void	flush() Flush the batcher and send all remaining items in memory to the database.
int	getTotalInsertCount() Get the total number of mappings to raw data create by this mapper.
int	insert(AbstractSqlQuery query) Insert mapping to raw spots using a query.
void	insert(short column, int position, RawData rawData) Link a spot to a raw data.
(package private) void	onBeforeClose() Update bytes on data cube 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 Detail

dataCube

private final DataCube dataCube

The datacube this batcher inserts data for.

noRawMapping

private final boolean noRawMapping

If the data cube has already received it's data and no raw data can be linked.

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.

bytes

private long bytes

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

bytesPerRow

private final long bytesPerRow

The number of bytes used by a single row.

rawMappingSql

private PreparedStatement rawMappingSql

The statement that inserts the spot/raw data link.

INSERT INTO Dynamic#RawParents (cube, column, position, rawdata_id)
VALUES (cube, ?, ?, ?)

rawMappingSqlStatement

private String rawMappingSqlStatement

The SQL string for the rawMappingSql statement.

Constructor Detail

MappingBatcher

MappingBatcher(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 Detail

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 on data cube and close open SQL statements.

Overrides:

onBeforeClose in class AbstractBatcher

Throws:

BaseException

insert

public void insert(short column,
                   int position,
                   RawData rawData)
            throws BaseException

Link a spot to a raw data. One spot may be linked to several raw data items.

Parameters:

column - The column coordinate of the spot

position - The position coordinate of the spot

rawData - The raw data object

Throws:

InvalidDataException - If the raw data is null

BaseException - If there is an error

insert

public int insert(AbstractSqlQuery query)
           throws BaseException

Insert mapping to raw spots using a query. The query MUST select data in the following order: column, position, rawDataId

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

getTotalInsertCount

public int getTotalInsertCount()

Get the total number of mappings to raw data create by this mapper.

Since:

2.2

buildRawMappingSql

private void buildRawMappingSql()
                         throws SQLException,
                                BaseException

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

Parameters:

selectSql - The SELECT part of the query

Throws:

BaseException

See Also:

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