net.sf.basedb.core
Class FilterBatcher

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

All Implemented Interfaces:

Batcher

public class FilterBatcher
extends AbstractBatcher

Batcher class for filtered bioassaysets. A filtered bioassayset is normally the result of a filtering transformation and uses the same data cube and layer as the source bioassayset to store it's data. This batcher is used to specify the column/position coordinates of the original spots that remains after the filter has been applied.

Code example: Filter spots where ch1 <= 2 * ch2

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

// Create new transformation and bioassayset to hold the
// filtered result
Transformation t = source.newTransformation();
dc.saveItem(t);
BioAssaySet filtered = t.newProduct(null, null, true);
dc.saveItem(filtered);

// Create a query that selects the column
// and position of all spots where ch1 > 2 * ch2
DynamicSpotQuery query = source.getSpotData();
query.select(Dynamic.select(VirtualColumn.COLUMN));
query.select(Dynamic.select(VirtualColumn.POSITION));
query.restrict(
   Restriction.gt(
      Dynamic.column(VirtualColumn.channel(1)),
      Expressions.multiply(
         Expressions.integer(2),
         Dynamic.column(VirtualColumn.channel(2))
      )
   )
);

// Execute the query, and use the batcher to insert the result
FilterBatcher batcher = filtered.getFilterBatcher();
DynamicResultIterator result = query.iterate(dc);
int column = result.getIndex(VirtualColumn.COLUMN.getName());
int position = result.getIndex(VirtualColumn.POSITION.getName());
while (result.hasNext())
{
   SqlResult r = result.next();
   batcher.insert(r.getShort(column), r.getInt(position));
}

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

Version:

2.0

Author:

Nicklas

See Also:

BioAssaySet.getFilterBatcher()

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 PreparedStatement	filterSql The statement that inserts filter data.
private String	filterSqlStatement The SQL string for the filterSql 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

FilterBatcher(DbControl dc, BioAssaySet bioAssaySet)
Create a new filter batcher for a bioassayset.

Method Summary

private void	buildFilterSql() Builds the insert SQL statement.
private String	buildInsertSelectSql(String selectSql) Build the INSERT INTO ...
void	flush() Flush the batcher and send all remaining items in memory to the database.
int	insert(AbstractSqlQuery query) Insert column/position coordinates using a query.
void	insert(short column, int position) Insert a column/position coordinate that passed the filter.
(package private) void	onBeforeClose() 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.

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.

filterSql

private PreparedStatement filterSql

The statement that inserts filter data.

INSERT INTO Dynamic#Filter (cube, filter, column, position)
VALUES (cube, filter, ?, ?)

filterSqlStatement

private String filterSqlStatement

The SQL string for the filterSql statement.

Constructor Detail

FilterBatcher

FilterBatcher(DbControl dc,
              BioAssaySet bioAssaySet)

Create a new filter 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

Close open SQL statements.

Overrides:

onBeforeClose in class AbstractBatcher

Throws:

BaseException

insert

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

Insert a column/position coordinate that passed the filter.

Parameters:

column - The column number

position - The position number

Throws:

BaseException - If there is an error

insert

public int insert(AbstractSqlQuery query)
           throws BaseException

Insert column/position coordinates using a query. The query MUST select data in the following order: column, position

Internally this method converts the query into a INSERT INTO ... SELECT ... query, making it very fast, since the data for each coordinate 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
// filtered result
Transformation t = source.newTransformation();
dc.saveItem(t);
BioAssaySet filtered = t.newProduct(null, null, true);
dc.saveItem(filtered);

// Create a query that selects the column
// and position of all spots where ch1 > 2 * ch2
DynamicSpotQuery query = source.getSpotData();
query.select(Dynamic.select(VirtualColumn.COLUMN));
query.select(Dynamic.select(VirtualColumn.POSITION));
query.restrict(
   Restriction.gt(
      Dynamic.column(VirtualColumn.channel(1)),
      Expressions.multiply(
         Expressions.integer(2),
         Dynamic.column(VirtualColumn.channel(2))
      )
   )
);

// Execute the query, and use the batcher to insert the result
FilterBatcher batcher = filtered.getFilterBatcher();
batcher.insert(query);

// Close, save 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

buildFilterSql

private void buildFilterSql()
                     throws SQLException,
                            BaseException

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

Parameters:

selectSql - The SELECT part of the query

Throws:

BaseException

See Also:

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