Package net.sf.basedb.core

Class MappingBatcher

java.lang.Object
net.sf.basedb.core.AbstractBatcher
net.sf.basedb.core.MappingBatcher
All Implemented Interfaces:
AutoCloseable, Batcher
public class MappingBatcher
extends AbstractBatcher
Batcher class for inserting parent mapping information in the dynamic database. This batcher is used to map data cube spots to their parent RawData.

Code example: Dynamic API - Creating a root bioassayset

Version:
2.0
Author:
Nicklas
See Also:
BioAssaySet.getMappingBatcher()
Last modified
$Date: 2015-04-21 09:59:42 +0200 (ti, 21 apr 2015) $

  • Field Details

    • dataCube

      private final DataCube dataCube
      The datacube this batcher inserts data for.

    • noRawMapping

      private final boolean noRawMapping
      If the data cube has already received it's data and no raw data can be linked.

    • 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.

    • rawMappingSql

      private PreparedStatement rawMappingSql
      The statement that inserts the spot/raw data link. 
      INSERT INTO Dynamic#RawParents (cube, column, position, rawdata_id)
VALUES (cube, ?, ?, ?)

    • rawMappingSqlStatement

      private String rawMappingSqlStatement
      The SQL string for the rawMappingSql statement.

  • Constructor Details

    • MappingBatcher

      MappingBatcher​(DbControl dc, DataCube dataCube)
      Create a new position batcher for a data cube. It is assumed that the calling code has checked that the cube 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
      Update bytes on data cube and close open SQL statements.
      Overrides:
      onBeforeClose in class AbstractBatcher
      Throws:
      BaseException

    • insert

      public void insert​(short column, int position, RawData rawData) throws BaseException
      Link a spot to a raw data. One spot may be linked to several raw data items.
      Parameters:
      column - The column coordinate of the spot
      position - The position coordinate of the spot
      rawData - The raw data object
      Throws:
      InvalidDataException - If the raw data is null
      BaseException - If there is an error

    • insert

      public int insert​(AbstractSqlQuery query) throws BaseException
      Insert mapping to raw spots using a query. The query MUST select data in the following order: column, position, rawDataId

      Internally this method converts the query into a INSERT INTO ... SELECT ... query, making it very fast, since the data for each position 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.

      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

    • getTotalInsertCount

      public int getTotalInsertCount()
      Get the total number of mappings to raw data create by this mapper.
      Since:
      2.2

    • buildRawMappingSql

      private void buildRawMappingSql() throws SQLException, BaseException
      Builds the insert SQL statement. Also creates the Dynamic#RawParents 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#RawParents table if it doesn't exists.
      Parameters:
      selectSql - The SELECT part of the query
      Throws:
      BaseException
      See Also:
      BatchUtil.buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String)