net.sf.basedb.core
Class SpotBatcher

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

All Implemented Interfaces:

Batcher

public class SpotBatcher
extends AbstractBatcher

Batcher class for per-spot intensity values for bioassaysets. This batcher is normally used when a new bioassayset has been created that uses a different cube and/or layer to store it's data than the source bioassayset.

Code example: Swap the intensities of channel 1 and 2

// Get source bioassayset
DbControl dc = ...
BioAssaySet source = ...

// Create new transformation and bioassayset to hold the
// new intensities, we use the same data cube as the source
// but a different layer
Transformation t = source.newTransformation();
dc.saveItem(t);
BioAssaySet bas = t.newProduct(null, "new", true);
dc.saveItem(bas);

// Create a query that selects the data of
// the source bioassayset
DynamicSpotQuery query = source.getSpotData();

// Execute the query, and use the batcher to swap the
// intensities
SpotBatcher batcher = bas.getSpotBatcher();
DynamicResultIterator result = query.iterate(dc);
int column = result.getIndex(VirtualColumn.COLUMN.getName());
int position = result.getIndex(VirtualColumn.POSITION.getName());
int ch1 = result.getIndex(VirtualColumn.channel(1).getName());
int ch2 = result.getIndex(VirtualColumn.channel(2).getName());
while (result.hasNext())
{
   SqlResult r = result.next();
   batcher.insert(r.getShort(column), r.getInt(position), 
      r.getFloat(ch2), r.getFloat(ch1));
}

// Close and commit
batcher.close();
dc.commit();

Version:

2.0

Author:

Nicklas

See Also:

BioAssaySet.getSpotBatcher()

Last modified

$Date: 2011-11-15 14:45:50 +0100 (Tue, 15 Nov 2011) $

Field Summary

private BioAssaySet	bioAssaySet The bioassayset this batcher inserts data for.
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 int	numChannels The number of channels used in the raw data type of the experiment where the bioassayset belongs.
private int	queuedInsertCount The number of queued inserts.
private PreparedStatement	spotSql The statement that inserts spot data.
private String	spotSqlStatement The SQL string for the spotSql 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

SpotBatcher(DbControl dc, BioAssaySet bioAssaySet)
Create a new spot batcher for a bioassayset.

Method Summary

private String	buildInsertSelectSql(String selectSql) Build the INSERT INTO ...
private void	buildSpotSql() Builds the insert SQL statement.
void	flush() Flush the batcher and send all remaining items in memory to the database.
int	insert(AbstractSqlQuery query) Insert spot intensities using a query.
void	insert(short column, int position, float... intensities) Insert intensities for a given column/position coordinate.
(package private) void	onBeforeClose() Update disk usage 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

bioAssaySet

private final BioAssaySet bioAssaySet

The bioassayset this batcher inserts data for.

numChannels

private final int numChannels

The number of channels used in the raw data type of the experiment where the bioassayset belongs.

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.

spotSql

private PreparedStatement spotSql

The statement that inserts spot data.

INSERT INTO Dynamic#PerSpot (cube, layer, column, position, ch1, ch2, ...)
VALUES (cube, layer, ?, ?, ?, ?, ...)

spotSqlStatement

private String spotSqlStatement

The SQL string for the spotSql statement.

Constructor Detail

SpotBatcher

SpotBatcher(DbControl dc,
            BioAssaySet bioAssaySet)

Create a new spot batcher for a bioassayset. It is assumed that the calling code has checked that the bioassayset is allowed to receive more data (ie. it's data cube layer 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 disk usage and close open SQL statements

Overrides:

onBeforeClose in class AbstractBatcher

Throws:

BaseException

insert

public void insert(short column,
                   int position,
                   float... intensities)
            throws BaseException

Insert intensities for a given column/position coordinate.

Parameters:

column - The column coordinate

position - The position coordinate

intensities - An array holding the intensities for the coordinate, the length must match the number of channels of the raw data type

Throws:

InvalidDataException - If the intensities array is null or of the incorrect length

BaseException - If there is another error

insert

public int insert(AbstractSqlQuery query)
           throws BaseException

Insert spot intensities using a query. The query MUST select data in the following order: column, position, ch1, ch2, ...

Internally this method converts the query into a INSERT INTO ... SELECT ... query, making it very fast, since the data for each spot 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.

Here is an alternative to the example above:

// Get source bioassayset
DbControl dc = ...
BioAssaySet source = ...

// Create new transformation and bioassayset to hold the
// new intensities, we use the same data cube as the source
// but a different layer
Transformation t = source.newTransformation();
dc.saveItem(t);
BioAssaySet bas = t.newProduct(null, "new", true);
dc.saveItem(bas);

// Create a query that selects the data of
// the source bioassayset, swap the order of the channels
DynamicSpotQuery query = source.getSpotData();
query.select(Dynamic.select(VirtualColumn.COLUMN));
query.select(Dynamic.select(VirtualColumn.POSITION));
query.select(Dynamic.select(VirtualColumn.channel(2)));
query.select(Dynamic.select(VirtualColumn.channel(1)));

// Execute the query, and use the batcher to insert the result
SpotBatcher batcher = bas.getSpotBatcher();
batcher.insert(query);

// Close and commit
batcher.close();
dc.commit();

Parameters:

query - The query that selects the data to be inserted

Returns:

int The number of spots inserted

Throws:

BaseException - If there is an error

buildSpotSql

private void buildSpotSql()
                   throws SQLException,
                          BaseException

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

Parameters:

selectSql - The SELECT part of the query

Throws:

BaseException

See Also:

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