Class SampleCoexpressionAnalysisServiceImpl

java.lang.Object

ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl

All Implemented Interfaces:

SampleCoexpressionAnalysisService

@Service
public class SampleCoexpressionAnalysisServiceImpl
extends Object
implements SampleCoexpressionAnalysisService

Manage the "sample correlation/coexpression" matrices.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
SampleCoexpressionAnalysisServiceImpl()

Method Summary

Modifier and Type	Method	Description
DoubleMatrix<BioAssay,BioAssay>	compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)	Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing using Isolation.SERIALIZABLE transaction isolation level.
boolean	hasAnalysis(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	loadBestMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	loadFullMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	loadRegressedMatrix(ExpressionExperiment ee)	Load the regressed coexpression matrix for the given experiment.
PreparedCoexMatrices	prepare(ExpressionExperiment ee)	🛑 Propagation.NEVER, and it has to be: this is where the time goes.
void	removeForExperiment(ExpressionExperiment ee)	Removes all coexpression matrices for the given experiment.
DoubleMatrix<BioAssay,BioAssay>	retrieveExisting(ExpressionExperiment ee)

Methods inherited from class Object

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

Constructor Details

SampleCoexpressionAnalysisServiceImpl

public SampleCoexpressionAnalysisServiceImpl()

Method Details

loadFullMatrix

@Transactional(readOnly=true)
public DoubleMatrix<BioAssay,BioAssay> loadFullMatrix(ExpressionExperiment ee)

Description copied from interface: SampleCoexpressionAnalysisService

Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix. If the analysis or the matrix does not exist, computes it.

Specified by:

loadFullMatrix in interface SampleCoexpressionAnalysisService

Parameters:

ee - the experiment to load the raw coexpression matrix for.

Returns:

the full, non-regressed matrix. If the matrix is not available event after attempted computation, returns null.

loadRegressedMatrix

@Transactional(readOnly=true)
public DoubleMatrix<BioAssay,BioAssay> loadRegressedMatrix(ExpressionExperiment ee)

Description copied from interface: SampleCoexpressionAnalysisService

Load the regressed coexpression matrix for the given experiment.

Specified by:

loadRegressedMatrix in interface SampleCoexpressionAnalysisService

Returns:

the regressed matrix if available, null might indicate that the is either no analysis or no regressed matrix, use SampleCoexpressionAnalysisService.hasAnalysis(ExpressionExperiment) to tell these apart.

loadBestMatrix

@Transactional(readOnly=true)
public DoubleMatrix<BioAssay,BioAssay> loadBestMatrix(ExpressionExperiment ee)

Description copied from interface: SampleCoexpressionAnalysisService

Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix. If the analysis or the matrix does not exist, computes it. If there are problems loading or computing the regressed matrix (e.g. because the experiment has no experimental design), the full matrix is returned instead.

Specified by:

loadBestMatrix in interface SampleCoexpressionAnalysisService

Parameters:

ee - the experiment to load the regressed coexpression matrix for.

Returns:

sample correlation matrix with major factors regressed out, if such matrix exists for the given experiment. If not, the full non-regressed matrix is returned. If no matrix is available event after attempted computation, returns null.

retrieveExisting

@Transactional(readOnly=true)
public DoubleMatrix<BioAssay,BioAssay> retrieveExisting(ExpressionExperiment ee)

Specified by:

retrieveExisting in interface SampleCoexpressionAnalysisService

prepare

@Transactional(propagation=NEVER)
public PreparedCoexMatrices prepare(ExpressionExperiment ee)
                             throws FilteringException

🛑 Propagation.NEVER, and it has to be: this is where the time goes.

The two getMatrix legs run quantile normalization, an all-pairs correlation and a least-squares fit. On GSE260875 (34,330 x 1,090) that was 44 minutes, and with hibernate.connection.handling_mode = DELAYED_ACQUISITION_AND_HOLD a transaction around it pinned a pooled connection for the whole stretch without issuing a statement — against a pool that recycles at 30 minutes (gemma.db.hikari.maxLifetime). Every read below already goes through a service method with its own transaction, and compute(ExpressionExperiment, PreparedCoexMatrices) is the write with its own.

⚠️ NEVER is viral upward: a caller that is itself transactional will now fail at entry with IllegalTransactionStateException. That is the rule doing its job, not a regression to route around — the caller needs splitting too.

Specified by:

prepare in interface SampleCoexpressionAnalysisService

Throws:

FilteringException

compute

@Transactional(isolation=SERIALIZABLE)
public DoubleMatrix<BioAssay,BioAssay> compute(ExpressionExperiment ee,
 PreparedCoexMatrices matrices)

Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing using Isolation.SERIALIZABLE transaction isolation level. This annotation also has to be appled to other methods of this class that call compute() directly or indirectly. PP changed this to do more of the processing in a read-only transaction

Specified by:

compute in interface SampleCoexpressionAnalysisService

Parameters:

ee - the experiment to create a sample correlation matrix for.

Returns:

the regressed coexpression matrix if available, otherwise the full

hasAnalysis

@Transactional(readOnly=true)
public boolean hasAnalysis(ExpressionExperiment ee)

Specified by:

hasAnalysis in interface SampleCoexpressionAnalysisService

removeForExperiment

@Transactional
public void removeForExperiment(ExpressionExperiment ee)

Description copied from interface: SampleCoexpressionAnalysisService

Removes all coexpression matrices for the given experiment.

Specified by:

removeForExperiment in interface SampleCoexpressionAnalysisService

Parameters:

ee - the experiment to remove the analysis for.