Package ubic.gemma.core.analysis.report

Class ExpressionExperimentReportServiceImpl

java.lang.Object

ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, ExpressionExperimentReportService

@Service("expressionExperimentReportService")
public class ExpressionExperimentReportServiceImpl
extends Object
implements ExpressionExperimentReportService, org.springframework.beans.factory.InitializingBean

Handles creation, serialization and/or marshaling of reports about expression experiments. Reports are stored in ExpressionExperimentValueObjects.

Author:

jsantos, paul, klc

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentReportServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
void	evictFromCache(Long id)	Invalidate the cached 'report' for the experiment with the given id.
ExpressionExperimentDetailsValueObject	generateSummary(Long id)	Generate a value object that contain summary information about links, biomaterials, and datavectors
Collection<ExpressionExperimentDetailsValueObject>	generateSummaryObjects()	Generates reports on ALL experiments, including 'private' ones.
void	getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject> vos)	Populate information about how many annotations there are, and how many factor values there are.
void	populateEventInformation(Collection<ExpressionExperimentDetailsValueObject> vos)	Fills in event and security information from the database.
void	populateReportInformation(Collection<ExpressionExperimentDetailsValueObject> vos)	Fills in link analysis and differential expression analysis summaries, and other info from the report.
void	recalculateBatchInfo()	Recalculates the batch effect and batch confound information for datasets that have been updated in the last 24 hours.
void	recalculateExperimentBatchInfo(ExpressionExperiment ee)	Recalculates the batch effect and batch confound information for the given dataset.
Collection<ExpressionExperimentDetailsValueObject>	retrieveSummaryObjects(Collection<Long> ids)	retrieves a collection of cached value objects containing summary information

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionExperimentReportServiceImpl

public ExpressionExperimentReportServiceImpl()

Method Detail

afterPropertiesSet

public void afterPropertiesSet()

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

evictFromCache

public void evictFromCache(Long id)

Description copied from interface: ExpressionExperimentReportService

Invalidate the cached 'report' for the experiment with the given id. If it is not cached nothing happens.

Specified by:

evictFromCache in interface ExpressionExperimentReportService

Parameters:

id - the id of the entity to evict

generateSummary

@Transactional(readOnly=true)
public ExpressionExperimentDetailsValueObject generateSummary(Long id)

Description copied from interface: ExpressionExperimentReportService

Generate a value object that contain summary information about links, biomaterials, and datavectors

Specified by:

generateSummary in interface ExpressionExperimentReportService

Parameters:

id - the id of the ee to generate summary for

Returns:

details VO

generateSummaryObjects

@Secured("GROUP_AGENT")
@Transactional(propagation=NEVER)
public Collection<ExpressionExperimentDetailsValueObject> generateSummaryObjects()

Description copied from interface: ExpressionExperimentReportService

Generates reports on ALL experiments, including 'private' ones. This should only be run by administrators as it takes a while to run.

Specified by:

generateSummaryObjects in interface ExpressionExperimentReportService

getAnnotationInformation

@Transactional(readOnly=true)
public void getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject> vos)

Populate information about how many annotations there are, and how many factor values there are. Batch is not counted towards the number of factors

Specified by:

getAnnotationInformation in interface ExpressionExperimentReportService

populateEventInformation

@Transactional(readOnly=true)
public void populateEventInformation(Collection<ExpressionExperimentDetailsValueObject> vos)

Fills in event and security information from the database. This will only retrieve the latest event (if any). This is rather slow so should be avoided if the information isn't needed.

Specified by:

populateEventInformation in interface ExpressionExperimentReportService

populateReportInformation

@Transactional(readOnly=true)
public void populateReportInformation(Collection<ExpressionExperimentDetailsValueObject> vos)

Description copied from interface: ExpressionExperimentReportService

Fills in link analysis and differential expression analysis summaries, and other info from the report.

Specified by:

populateReportInformation in interface ExpressionExperimentReportService

Parameters:

vos - value objects

retrieveSummaryObjects

@Transactional(readOnly=true)
public Collection<ExpressionExperimentDetailsValueObject> retrieveSummaryObjects(Collection<Long> ids)

Description copied from interface: ExpressionExperimentReportService

retrieves a collection of cached value objects containing summary information

Specified by:

retrieveSummaryObjects in interface ExpressionExperimentReportService

Parameters:

ids - the ids of ees for which the summary objects should be retrieved.

Returns:

a collection of cached value objects

recalculateBatchInfo

@Secured("GROUP_AGENT")
@Transactional(propagation=NEVER)
public void recalculateBatchInfo()

Description copied from interface: ExpressionExperimentReportService

Recalculates the batch effect and batch confound information for datasets that have been updated in the last 24 hours.

Specified by:

recalculateBatchInfo in interface ExpressionExperimentReportService

recalculateExperimentBatchInfo

@Secured("GROUP_AGENT")
@Transactional
public void recalculateExperimentBatchInfo(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentReportService

Recalculates the batch effect and batch confound information for the given dataset.

Specified by:

recalculateExperimentBatchInfo in interface ExpressionExperimentReportService

Parameters:

ee - the experiment to recalculate the batch properties for.