Package net.sf.basedb.core

Class SpotExtraValueBatcher<I>

java.lang.Object
net.sf.basedb.core.AbstractBatcher
net.sf.basedb.core.SpotExtraValueBatcher<I>
All Implemented Interfaces:
AutoCloseable, 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:
Last modified
$Date: 2015-05-12 11:27:08 +0200 (ti, 12 maj 2015) $

  • Field Details

    • 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:

    • 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 Details

    • 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 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:

    • 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:
      BaseException - If there is another error
      InvalidDataException

    • 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:

    • 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: