Package ubic.gemma.persistence.service.maintenance

Class TableMaintenanceUtilImpl

java.lang.Object

ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl

All Implemented Interfaces:

TableMaintenanceUtil

@Service
public class TableMaintenanceUtilImpl
extends Object
implements TableMaintenanceUtil

Functions for maintaining the database. This is intended for denormalized tables and statistics tables that need to be generated periodically.

Author:

jsantos, paul

Field Summary

Fields inherited from interface ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil

EE2AD_QUERY_SPACE, EE2C_QUERY_SPACE, GENE2CS_BATCH_SIZE, GENE2CS_QUERY_SPACE

Constructor Summary

Constructors

Constructor	Description
TableMaintenanceUtilImpl()

Method Summary

Modifier and Type	Method	Description
void	disableEmail()	For use in tests.
void	evictEe2AdQueryCache()	Evict the query cache for the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.
void	evictEe2CQueryCache()	Evict the query cache for the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
void	evictGene2CsQueryCache()	Evict the query cache for the GENE2CS table.
int	updateExpressionExperiment2ArrayDesignEntries(Date sinceLastUpdate, boolean truncate)	Update the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.
int	updateExpressionExperiment2ArrayDesignEntries(ExpressionExperiment ee)
int	updateExpressionExperiment2CharacteristicEntries(Class<?> level, Date sinceLastUpdate, boolean truncate)	Update a specific level of the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
int	updateExpressionExperiment2CharacteristicEntries(Date sinceLastUpdate, boolean truncate)	Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.
int	updateExpressionExperiment2CharacteristicEntries(ExpressionExperiment ee, Class<?> level)	Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table for a specific experiment.
int	updateGene2CsEntries()	If necessary, update the GENE2CS table.
int	updateGene2CsEntries(Date sinceLastUpdate, boolean truncate, boolean force)	Update the GENE2CS table.
int	updateGene2CsEntries(ArrayDesign arrayDesign, boolean force)	Update the GENE2CS table for a specific ArrayDesign.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TableMaintenanceUtilImpl

public TableMaintenanceUtilImpl()

Method Details

updateGene2CsEntries

@Transactional
public int updateGene2CsEntries()

Description copied from interface: TableMaintenanceUtil

If necessary, update the GENE2CS table.

Specified by:

updateGene2CsEntries in interface TableMaintenanceUtil

updateGene2CsEntries

@Transactional
public int updateGene2CsEntries(ArrayDesign arrayDesign,
 boolean force)

Description copied from interface: TableMaintenanceUtil

Update the GENE2CS table for a specific ArrayDesign.

Specified by:

updateGene2CsEntries in interface TableMaintenanceUtil

Parameters:

arrayDesign - the platform for which to update the GENE2CS entries

force - update the table even if no platforms has been modified since the last update

updateGene2CsEntries

@Transactional
public int updateGene2CsEntries(@Nullable
 Date sinceLastUpdate,
 boolean truncate,
 boolean force)

Description copied from interface: TableMaintenanceUtil

Update the GENE2CS table.

Specified by:

updateGene2CsEntries in interface TableMaintenanceUtil

Parameters:

sinceLastUpdate - if not null, only update entries whose corresponding ArrayDesign hsa been updated after the given date

truncate - if true, the GENE2CS table will be truncated before the update

force - update the table even if no platforms has been modified since the last update

updateExpressionExperiment2CharacteristicEntries

@Transactional
public int updateExpressionExperiment2CharacteristicEntries(@Nullable
 Date sinceLastUpdate,
 boolean truncate)

Description copied from interface: TableMaintenanceUtil

Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.

Specified by:

updateExpressionExperiment2CharacteristicEntries in interface TableMaintenanceUtil

Returns:

the number of records that were created or updated

updateExpressionExperiment2CharacteristicEntries

@Transactional
public int updateExpressionExperiment2CharacteristicEntries(Class<?> level,
 @Nullable
 Date sinceLastUpdate,
 boolean truncate)

Description copied from interface: TableMaintenanceUtil

Update a specific level of the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.

Specified by:

updateExpressionExperiment2CharacteristicEntries in interface TableMaintenanceUtil

Parameters:

level - the level to update which is either ExpressionExperiment, BioMaterial or ExperimentalDesign

Returns:

the number of records that were created or updated

updateExpressionExperiment2CharacteristicEntries

@Transactional
public int updateExpressionExperiment2CharacteristicEntries(ExpressionExperiment ee,
 @Nullable
 Class<?> level)

Description copied from interface: TableMaintenanceUtil

Update the EXPRESSION_EXPERIMENT2CHARACTERISTIC table for a specific experiment.

Specified by:

updateExpressionExperiment2CharacteristicEntries in interface TableMaintenanceUtil

updateExpressionExperiment2ArrayDesignEntries

@Transactional
public int updateExpressionExperiment2ArrayDesignEntries(@Nullable
 Date sinceLastUpdate,
 boolean truncate)

Description copied from interface: TableMaintenanceUtil

Update the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.

Specified by:

updateExpressionExperiment2ArrayDesignEntries in interface TableMaintenanceUtil

Parameters:

sinceLastUpdate - only update entries for platforms updated since this date

truncate - if true, the table will be truncated before the update

Returns:

the number of records that were created or updated

updateExpressionExperiment2ArrayDesignEntries

@Transactional
public int updateExpressionExperiment2ArrayDesignEntries(ExpressionExperiment ee)

Specified by:

updateExpressionExperiment2ArrayDesignEntries in interface TableMaintenanceUtil

evictGene2CsQueryCache

public void evictGene2CsQueryCache()

Description copied from interface: TableMaintenanceUtil

Evict the query cache for the GENE2CS table.

Specified by:

evictGene2CsQueryCache in interface TableMaintenanceUtil

evictEe2CQueryCache

public void evictEe2CQueryCache()

Description copied from interface: TableMaintenanceUtil

Evict the query cache for the EXPRESSION_EXPERIMENT2CHARACTERISTIC table.

Specified by:

evictEe2CQueryCache in interface TableMaintenanceUtil

evictEe2AdQueryCache

public void evictEe2AdQueryCache()

Description copied from interface: TableMaintenanceUtil

Evict the query cache for the EXPRESSION_EXPERIMENT2_ARRAY_DESIGN table.

Specified by:

evictEe2AdQueryCache in interface TableMaintenanceUtil

disableEmail

public void disableEmail()

For use in tests.

Specified by:

disableEmail in interface TableMaintenanceUtil