Class BatchInfoPopulationServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl

All Implemented Interfaces:

BatchInfoPopulationService

@Service
public class BatchInfoPopulationServiceImpl
extends Object
implements BatchInfoPopulationService

Retrieve batch information from the data source, if possible, and populate it into experiments.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
BatchInfoPopulationServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	fillBatchInformation(ExpressionExperiment ee, boolean force)	Attempt to obtain batch information from the data provider and populate it into the given experiment.
void	setFastqHeadersDir(Path fastqHeadersDir)	Set the path to use to resolve FASTQ headers.

Methods inherited from class Object

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

Constructor Details

BatchInfoPopulationServiceImpl

public BatchInfoPopulationServiceImpl()

Method Details

fillBatchInformation

@Transactional
@AuditedOnError(value=BatchInformationMissingEvent.class,exception=BatchInfoMissingException.class) @AuditedOnError(FailedBatchInformationFetchingEvent.class)
public void fillBatchInformation(ExpressionExperiment ee,
 boolean force)
                          throws BatchInfoPopulationException

Description copied from interface: BatchInfoPopulationService

Attempt to obtain batch information from the data provider and populate it into the given experiment. The method used may vary. For GEO, the default method is to download the raw data files, and look in them for a date. This is not implemented for every possible type of raw data file. For RNA-seq, we look for FASTQ headers under the configured FASTQ_HEADERS_ROOT.

Specified by:

fillBatchInformation in interface BatchInfoPopulationService

Parameters:

ee - the experiment

force - whether to force recomputation

Throws:

BatchInfoPopulationException - describing the issue with populating batch information

setFastqHeadersDir

public void setFastqHeadersDir(Path fastqHeadersDir)

Description copied from interface: BatchInfoPopulationService

Set the path to use to resolve FASTQ headers.

Exposed for testing, do not use in production code.

Specified by:

setFastqHeadersDir in interface BatchInfoPopulationService