Class ExpressionExperimentPlatformSwitchService

java.lang.Object

ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService

@Service
public class ExpressionExperimentPlatformSwitchService
extends Object

Switch an expression experiment from one array design to another. This is valuable when the EE uses more than on AD, and a merged AD exists. The following steps are needed:

• Delete old analyses of this experiment and processeddata vectors
• For each array design, for each probe, identify the matching probe on the merged AD. Have to deal with situation
• where more than one occurrence of each sequence is found.
• all DEDVs must be switched to use the new AD's design elements
• all bioassays must be switched to the new AD.
• update the EE description
• commit changes.
• Computed processed data vectors

This also handles the case of multisamples-per-platform - NOT the case of one-sample-per-platform but multiple platforms; for that you have to run VectorMerging. For more nutty situations this will probably create a mess.

Author:

pavlidis

See Also:

• VectorMergingService

Field Summary

Fields

Modifier and Type	Field	Description
static final BioSequence	NULL_BIOSEQUENCE	Used to identify design elements that have no sequence associated with them.

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentPlatformSwitchService()

Method Summary

Modifier and Type	Method	Description
ArrayDesign	locateMergedDesign(ExpressionExperiment expExp)
void	switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign)	If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform
ArrayDesign	switchExperimentToMergedPlatform(ExpressionExperiment expExp)	Automatically identify an appropriate merged platform
boolean	switchPlatformAndVectors(ExpressionExperiment ee, ArrayDesign arrayDesign)	The transactional part of switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign): everything except regenerating the processed vectors.

Methods inherited from class Object

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

Field Details

NULL_BIOSEQUENCE

public static final BioSequence NULL_BIOSEQUENCE

Used to identify design elements that have no sequence associated with them.

Constructor Details

ExpressionExperimentPlatformSwitchService

public ExpressionExperimentPlatformSwitchService()

Method Details

switchExperimentToArrayDesign

@Transactional(propagation=NEVER)
@Audited(value=ExpressionExperimentPlatformSwitchEvent.class,
         messageSpel="'Switch to use ' + #arrayDesign.shortName")
public void switchExperimentToArrayDesign(ExpressionExperiment ee,
 ArrayDesign arrayDesign)

If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform

Propagation.NEVER: the switch commits in its own transaction, and the processed vectors are then regenerated with none open, because ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment, boolean) is itself NEVER and throws when called inside one.

Parameters:

ee - ee

arrayDesign - The array design to switch to. If some samples already use that array design, nothing will be changed for them.

switchPlatformAndVectors

@Transactional
public boolean switchPlatformAndVectors(ExpressionExperiment ee,
 ArrayDesign arrayDesign)

The transactional part of switchExperimentToArrayDesign(ExpressionExperiment, ArrayDesign): everything except regenerating the processed vectors.

Returns:

true if the experiment has data on a multi-platform-per-sample design, in which case its processed vectors must be regenerated

switchExperimentToMergedPlatform

@Transactional(propagation=NEVER)
public ArrayDesign switchExperimentToMergedPlatform(ExpressionExperiment expExp)

Automatically identify an appropriate merged platform

Parameters:

expExp - the experiment to switch to a merged platform

Returns:

the selected merged platform the experiment was switched to

locateMergedDesign

@Transactional(readOnly=true)
public ArrayDesign locateMergedDesign(ExpressionExperiment expExp)