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

Class GeoServiceImpl

java.lang.Object

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

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, GeoService

@Component
public class GeoServiceImpl
extends Object
implements GeoService, org.springframework.beans.factory.InitializingBean

Non-interactive fetching, processing and persisting of GEO data.

Author:

pavlidis

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.loader.expression.geo.service.GeoService

GeoService.GeoUpdateConfig

Constructor Summary

Constructors

Constructor	Description
GeoServiceImpl()

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.
void	afterPropertiesSet()
Collection<?>	fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform)	Load data, no restrictions on superseries or subseries
Collection<?>	fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform, boolean allowSuperSeriesImport, boolean allowSubSeriesImport)	Given a GEO GSE or GDS (or GPL, but support might not be complete) Check that it doesn't already exist in the system, filter samples Download and parse GDS files and GSE file needed Convert the GDS and GSE into a ExpressionExperiment (or just the ArrayDesigns) Load the resulting ExpressionExperiment and/or ArrayDesigns into Gemma
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 ee, GeoService.GeoUpdateConfig geoUpdateConfig)	Refetch and reprocess a given experiment.

Methods inherited from class java.lang.Object

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

Constructor Details

GeoServiceImpl

public GeoServiceImpl()

Method Details

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

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

Throws:

Exception

addElements

@Transactional
public ArrayDesign addElements(ArrayDesign targetPlatform)

Description copied from interface: GeoService

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

Specified by:

addElements in interface GeoService

Parameters:

targetPlatform - already persistent array design.

Returns:

updated (persistent) array design

fetchAndLoad

@Transactional
public Collection<?> fetchAndLoad(String geoAccession,
 boolean loadPlatformOnly,
 boolean doSampleMatching,
 boolean splitByPlatform)

Description copied from interface: GeoService

Load data, no restrictions on superseries or subseries

Specified by:

fetchAndLoad in interface GeoService

Parameters:

geoAccession - accession

loadPlatformOnly - load platforms only

doSampleMatching - do sample matching

splitByPlatform - split incompatible platforms

Returns:

collection

fetchAndLoad

@Transactional
public Collection<?> fetchAndLoad(String geoAccession,
 boolean loadPlatformOnly,
 boolean doSampleMatching,
 boolean splitByPlatform,
 boolean allowSuperSeriesImport,
 boolean allowSubSeriesImport)

Given a GEO GSE or GDS (or GPL, but support might not be complete)

1. Check that it doesn't already exist in the system, filter samples
2. Download and parse GDS files and GSE file needed
3. Convert the GDS and GSE into a ExpressionExperiment (or just the ArrayDesigns)
4. Load the resulting ExpressionExperiment and/or ArrayDesigns into Gemma

Specified by:

fetchAndLoad in interface GeoService

Parameters:

geoAccession - accession

loadPlatformOnly - load platforms only

doSampleMatching - do sample matching

splitByPlatform - split incompatible platforms

allowSuperSeriesImport - Allow loading if the Series is a SuperSeries

allowSubSeriesImport - Allow loading if the Series is a SubSeries

Returns:

collection

updateFromGEO

@Transactional
public void updateFromGEO(String geoAccession,
 GeoService.GeoUpdateConfig geoUpdateConfig)

Description copied from interface: GeoService

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 GeoService.updateFromGEO(ExpressionExperiment, GeoUpdateConfig).

Specified by:

updateFromGEO in interface GeoService

updateFromGEO

public void updateFromGEO(ExpressionExperiment ee,
 GeoService.GeoUpdateConfig geoUpdateConfig)

Description copied from interface: GeoService

Refetch and reprocess a given experiment.

Specified by:

updateFromGEO in interface GeoService

loadFromSoftFile

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

Description copied from interface: GeoService

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

Specified by:

loadFromSoftFile in interface GeoService

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

public void setGeoDomainObjectGenerator(GeoDomainObjectGenerator generator)

Specified by:

setGeoDomainObjectGenerator in interface GeoService