Package net.sf.basedb.core

Class FilterBatcher

java.lang.Object
net.sf.basedb.core.AbstractBatcher
net.sf.basedb.core.FilterBatcher
All Implemented Interfaces:
AutoCloseable, 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: 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.

    • 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 Details

    • 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 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
      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)