Package net.sf.basedb.core

Class SpotBatcher

java.lang.Object
net.sf.basedb.core.AbstractBatcher
net.sf.basedb.core.SpotBatcher
All Implemented Interfaces:
AutoCloseable, 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: 2014-06-10 15:52:45 +0200 (ti, 10 jun 2014) $

  • Field Details

    • 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 Details

    • 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 Details

    • 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)