public class FilterBatcher extends AbstractBatcher
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();
BioAssaySet.getFilterBatcher()
Modifier and Type | Field and Description |
---|---|
private BioAssaySet |
bioAssaySet
The bioassayset this batcher inserts data for.
|
private long |
bytes
The number of bytes this batcher has added to the experiment.
|
private long |
bytesPerRow
The number of bytes used by a single row.
|
private PreparedStatement |
filterSql
The statement that inserts filter data.
|
private String |
filterSqlStatement
The SQL string for the
filterSql statement. |
private int |
queuedInsertCount
The number of queued inserts.
|
private int |
totalInsertCount
The total number of inserts done by this batcher.
|
debugSqlEnabled, logSql
Constructor and Description |
---|
FilterBatcher(DbControl dc,
BioAssaySet bioAssaySet)
Create a new filter batcher for a bioassayset.
|
Modifier and Type | Method and Description |
---|---|
private void |
buildFilterSql()
Builds the insert SQL statement.
|
private String |
buildInsertSelectSql(String selectSql)
Build the INSERT INTO ...
|
void |
flush()
Flush the batcher and send all remaining items in memory to the
database.
|
int |
insert(AbstractSqlQuery query)
Insert column/position coordinates using a query.
|
void |
insert(short column,
int position)
Insert a column/position coordinate that passed the filter.
|
(package private) void |
onBeforeClose()
Close open SQL statements.
|
analyzeTable, close, getBatchSize, getDbControl, getSessionControl, isClosed, setBatchSize, setDbControl, updateLastAccess
private final BioAssaySet bioAssaySet
private int queuedInsertCount
private int totalInsertCount
private long bytes
private final long bytesPerRow
private PreparedStatement filterSql
INSERT INTO Dynamic#Filter (cube, filter, column, position) VALUES (cube, filter, ?, ?)
FilterBatcher(DbControl dc, BioAssaySet bioAssaySet)
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(short column, int position) throws BaseException
column
- The column numberposition
- The position numberBaseException
- 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 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();
query
- The query that selects the data to be insertedBaseException
- If there is an errorprivate void buildFilterSql() throws SQLException, BaseException
private String buildInsertSelectSql(String selectSql) throws BaseException
selectSql
- The SELECT part of the queryBaseException
BatchUtil.buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String)