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

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

All Implemented Interfaces:

Batcher

public class SpotExtraValueBatcher<I>
extends AbstractBatcher

Batcher class for per-spot 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 intensities of channel 1 and 2

// Get source bioassayset, extra value type and job(null can be used if no job)
DbControl dc = ...
BioAssaySet source = ...
ExtraValueType type = ...
Job job = ...

// 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 from
// the source bioassayset
DynamicSpotQuery query = source.getSpotData();

// Execute the query, and use the batcher to insert the new values
SpotExtraValueBatcher<Float> batcher = bas.getSpotExtraValueBatcher(Float.class, type, job);
DynamicResultIterator spots = query.iterate(dc);
int column = spots.getIndex(VirtualColumn.COLUMN.getName());
int position = spots.getIndex(VirtualColumn.POSITION.getName());
int ch1 = spots.getIndex(VirtualColumn.channel(1).getName());
int ch2 = spots.getIndex(VirtualColumn.channel(2).getName());
while (spots.hasNext())
{
   SqlResult r = spots.next();
   batcher.insert(r.getShort(column), r.getInt(position), 
      r.getFloat(ch1) * r.getFloat(ch2));
}

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

Version:

2.0

Author:

Nicklas

See Also:

BioAssaySet.getSpotExtraValueBatcher(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

SpotExtraValueBatcher(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.
ExtraValue	getExtraValue() Get the extra value item representing all extra values.
int	insert(AbstractSqlQuery query) Insert extra values using a query.
void	insert(short column, int position, I value) Insert an extra value 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

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#SpotExtraXxx (cube, extra, column, position, value)
VALUES (cube, extra, ?, ?, ?)

extraSqlStatement

private String extraSqlStatement

The SQL string for the extraSql statement.

Constructor Detail

SpotExtraValueBatcher

SpotExtraValueBatcher(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 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,
                   I value)
            throws InvalidDataException,
                   BaseException

Insert an extra value for a given column/position coordinate.

Parameters:

column - The column coordinate

position - The position coordinate

value - The extra value

Throws:

InvalidDataException

BaseException - If there is another error

insert

public int insert(AbstractSqlQuery query)
           throws BaseException

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

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.

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(short, 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 from
// the source bioassayset
DynamicSpotQuery query = source.getSpotData();
query.select(Dynamic.select(VirtualColumn.COLUMN));
query.select(Dynamic.select(VirtualColumn.POSITION));
Expression product = Expressions.multiply(
        Dynamic.column(VirtualColumn.channel(1)),
        Dynamic.column(VirtualColumn.channel(2))
);
query.select(Selections.expression(product, "product"));

// 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 spots inserted

Throws:

BaseException - If there is an error

getExtraValue

public ExtraValue getExtraValue()

Get the extra value item representing all extra values.

buildSpotSql

private void buildSpotSql()
                   throws SQLException,
                          BaseException

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

Parameters:

selectSql - The SELECT part of the query

Throws:

BaseException

See Also:

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