Package ubic.gemma.core.loader.expression.geo.service

Interface GeoService

All Known Implementing Classes:

GeoServiceImpl

public interface GeoService

Author:

paul

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	GeoService.GeoUpdateConfig

Method Summary

Modifier and Type	Method	Description
ArrayDesign	addElements(ArrayDesign targetPlatform)	For the rare cases (Exon arrays) where we load the platform in two stages.
Collection<?>	fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitIncompatiblePlatforms)	Load data, no restrictions on superseries or subseries
Collection<?>	fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitIncompatiblePlatforms, boolean allowSuperSeriesImport, boolean allowSubSeriesImport)
Collection<?>	loadFromSoftFile(String accession, String softFile, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform)	Load from a SOFT file.
void	setGeoDomainObjectGenerator(GeoDomainObjectGenerator generator)
void	updateFromGEO(String geoAccession, GeoService.GeoUpdateConfig geoUpdateConfig)	Refetch and reprocess the GEO series, updating select information.
void	updateFromGEO(ExpressionExperiment expressionExperiment, GeoService.GeoUpdateConfig geoUpdateConfig)	Refetch and reprocess a given experiment.

Method Detail

addElements

ArrayDesign addElements(ArrayDesign targetPlatform)

For the rare cases (Exon arrays) where we load the platform in two stages.

Parameters:

targetPlatform - already persistent array design.

Returns:

updated (persistent) array design

fetchAndLoad

Collection<?> fetchAndLoad(String geoAccession,
                           boolean loadPlatformOnly,
                           boolean doSampleMatching,
                           boolean splitIncompatiblePlatforms)

Load data, no restrictions on superseries or subseries

Parameters:

doSampleMatching - do sample matching

geoAccession - accession

loadPlatformOnly - load platforms only

splitIncompatiblePlatforms - split incompatible platforms

Returns:

collection

fetchAndLoad

Collection<?> fetchAndLoad(String geoAccession,
                           boolean loadPlatformOnly,
                           boolean doSampleMatching,
                           boolean splitIncompatiblePlatforms,
                           boolean allowSuperSeriesImport,
                           boolean allowSubSeriesImport)

Parameters:

allowSuperSeriesImport - Allow loading if the Series is a SuperSeries

allowSubSeriesImport - Allow loading if the Series is a SubSeries

doSampleMatching - do sample matching

geoAccession - accession

loadPlatformOnly - load platforms only

splitIncompatiblePlatforms - split incompatible platforms

Returns:

collection

updateFromGEO

void updateFromGEO(String geoAccession,
                   GeoService.GeoUpdateConfig geoUpdateConfig)

Refetch and reprocess the GEO series, updating select information. Currently only implemented for experiments (GSEs)

All experiments that uses the GEO accession will be updated as per updateFromGEO(ExpressionExperiment, GeoUpdateConfig).

updateFromGEO

void updateFromGEO(ExpressionExperiment expressionExperiment,
                   GeoService.GeoUpdateConfig geoUpdateConfig)

Refetch and reprocess a given experiment.

loadFromSoftFile

Collection<?> loadFromSoftFile(String accession,
                               String softFile,
                               boolean loadPlatformOnly,
                               boolean doSampleMatching,
                               boolean splitByPlatform)

Load from a SOFT file. This can be used for testing but maybe there are other situations it is useful.

Parameters:

accession - e.g GSE1234

softFile - the full path to the SOFT file. The file name has to be [accession].soft.gz

Returns:

a single experiment.

setGeoDomainObjectGenerator

void setGeoDomainObjectGenerator(GeoDomainObjectGenerator generator)