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java.lang.Object net.sf.basedb.core.AbstractBatcher net.sf.basedb.core.PositionBatcher
public class PositionBatcher
Batcher class for per-position data in the dynamic database. This batcher is used to insert data that is valid for all positions in a data cube.
Normally this means linking a position to a reporter.
Code example: Dynamic API - Creating a root bioassayset
BioAssaySet.getPositionBatcher()
Field Summary | |
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private long |
bytes
The number of bytes this batcher has added to the data cube and experiment. |
private long |
bytesPerRow
The number of bytes used by a single row. |
private DataCube |
dataCube
The datacube this batcher inserts data for. |
private int |
maxPosition
The maximum position number inserted by the batcher. |
private PreparedStatement |
positionSql
The statement that inserts the position/reporter link. |
private String |
positionSqlStatement
The SQL string for the positionSql 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 |
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debugSqlEnabled, logSql |
Constructor Summary | |
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PositionBatcher(DbControl dc,
DataCube dataCube)
Create a new position batcher for a data cube. |
Method Summary | |
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private String |
buildInsertSelectSql(String selectSql)
Build the INSERT INTO ... |
private void |
buildPositionSql()
Builds the insert SQL statement. |
void |
flush()
Flush the batcher and send all remaining items in memory to the database. |
int |
insert(AbstractSqlQuery query)
Insert position/reporter links using a query. |
void |
insert(int position,
ReporterData reporter)
Link a position to a reporter. |
(package private) void |
onBeforeClose()
Update bytes and max position on the datacube and close open SQL statements. |
Methods inherited from class net.sf.basedb.core.AbstractBatcher |
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analyzeTable, close, getBatchSize, getDbControl, getSessionControl, isClosed, setBatchSize, setDbControl, updateLastAccess |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final DataCube dataCube
private int queuedInsertCount
private int totalInsertCount
private int maxPosition
private long bytes
private final long bytesPerRow
private PreparedStatement positionSql
INSERT INTO Dynamic#PerPosition (cube, position, reporter_id) VALUES (cube, ?, ?)
private String positionSqlStatement
positionSql
statement.
Constructor Detail |
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PositionBatcher(DbControl dc, DataCube dataCube)
Method Detail |
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public void flush() throws BaseException
Batcher
BaseException
- If there is an errorBatcher.close()
void onBeforeClose() throws BaseException
onBeforeClose
in class AbstractBatcher
BaseException
public void insert(int position, ReporterData reporter) throws BaseException
position
- The position coordinatereporter
- The reporter or null if no reporter is known
BaseException
- If there is an errorpublic int insert(AbstractSqlQuery query) throws BaseException
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.
query
- The query that selects the data to be inserted
BaseException
- If there is an errorprivate void buildPositionSql() throws SQLException, BaseException
SQLException
BaseException
BatchUtil.buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[])
private String buildInsertSelectSql(String selectSql) throws BaseException
selectSql
- The SELECT part of the query
BaseException
BatchUtil.buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String)
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