net.sf.basedb.core
Class PositionExtraValueBatcher<I>

java.lang.Object
  net.sf.basedb.core.AbstractBatcher
      net.sf.basedb.core.PositionExtraValueBatcher<I>

All Implemented Interfaces:

Batcher

public class PositionExtraValueBatcher<I>
extends AbstractBatcher

Batcher class for per-position extra values. This batcher can only be used for a new bioassayset that hasn't yet been committed to the database.

Code example: Multiply the mean of intensities of channel 1 and 2

// Get source bioassayset and extra value type
DbControl dc = ...
BioAssaySet source = ...
ExtraValueType type = ...

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

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

// Multiply the mean of the intensities
Expression meanCh1 = Aggregations.mean(Dynamic.column(VirtualColumn.channel(1)));
Expression meanCh2 = Aggregations.mean(Dynamic.column(VirtualColumn.channel(2)));
Expression product = Expressions.multiply(meanCh1, meanCh2);

// Select the position and product, and group by position
query.select(Dynamic.select(VirtualColumn.POSITION));
query.select(Selects.expression(product, "product"));
query.group(Dynamic.column(VirtualColumn.POSITION));

// Execute the query, and use the batcher to insert the new values
SpotExtraValueBatcher<Float> batcher = bas.getSpotExtraValueBatcher(Float.class, type);
DynamicResultIterator spots = query.iterate(dc);
int position = spots.getIndex(VirtualColumn.POSITION.getName());
int prod = spots.getIndex("product");
while (spots.hasNext())
{
   SqlResult r = spots.next();
   batcher.insert(r.getInt(position), r.getFloat(prod));
}

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

Version:

2.0

Author:

Nicklas

See Also:

BioAssaySet.getPositionExtraValueBatcher(Class, ExtraValueType, Job)

Last modified

$Date: 2010-01-18 08:31:09 +0100 (Mon, 18 Jan 2010) $

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 PreparedStatement	extraSql The statement that inserts spot data.
private String	extraSqlStatement The SQL string for the extraSql statement.
private ExtraValue	extraValue The extra value object which links the extra value type.
private int	queuedInsertCount The number of queued inserts.
private int	sqlType The sql type code of the value to insert.
private int	totalInsertCount The total number of inserts done by this batcher.
private Type	valueType The type of values to insert.

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

debugSqlEnabled, logSql

Constructor Summary

PositionExtraValueBatcher(DbControl dc, ExtraValue extraValue)
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 position extra values using a query.
void	insert(int position, I value) Insert an extra value for a given 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

extraValue

private final ExtraValue extraValue

The extra value object which links the extra value type.

valueType

private final Type valueType

The type of values to insert.

sqlType

private final int sqlType

The sql type code of the value to insert.

See Also:

Types

bytesPerRow

private final long bytesPerRow

The number of bytes used by a single row.

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.

extraSql

private PreparedStatement extraSql

The statement that inserts spot data.

INSERT INTO Dynamic#PositionExtraXxx (cube, extra, position, value)
VALUES (cube, extra, ?, ?)

extraSqlStatement

private String extraSqlStatement

The SQL string for the extraSql statement.

Constructor Detail

PositionExtraValueBatcher

PositionExtraValueBatcher(DbControl dc,
                          ExtraValue extraValue)

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(int position,
                   I value)
            throws InvalidDataException,
                   BaseException

Insert an extra value for a given position coordinate.

Parameters:

position - The position coordinate

value - The extra value

Throws:

InvalidDataException - If some data is corrupted

BaseException - If there is another error

insert

public int insert(AbstractSqlQuery query)
           throws BaseException

Insert position extra values using a query. The query MUST select data in the following order: position, extraValue

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.

Note! This method can't be called for string extra values. This is because the length of each string must be added to the disk usage. So they must be processed individually in any case. Use the other insert(int, Object) method.

Here is an alternative to the example above:

// Get source bioassayset and extra value type
DbControl dc = ...
BioAssaySet source = ...
ExtraValueType type = ...

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


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

// Multiply the mean of the intensities
Expression meanCh1 = Aggregations.mean(Dynamic.column(VirtualColumn.channel(1)));
Expression meanCh2 = Aggregations.mean(Dynamic.column(VirtualColumn.channel(2)));
Expression product = Expressions.multiply(meanCh1, meanCh2);

// Select the position and product, and group by position
query.select(Dynamic.select(VirtualColumn.POSITION));
query.select(Selects.expression(product, "product"));
query.group(Dynamic.column(VirtualColumn.POSITION));

// Execute the query, and use the batcher to insert the new values
SpotExtraValueBatcher<Float> batcher = bas.getSpotExtraValueBatcher(Float.class, type);
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 rows inserted

Throws:

BaseException - If there is an error

buildSpotSql

private void buildSpotSql()
                   throws SQLException,
                          BaseException

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

Parameters:

selectSql - The SELECT part of the query

Throws:

BaseException

See Also:

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