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

Class GeoServiceImpl

java.lang.Object

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

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

All Implemented Interfaces:

Aware, BeanFactoryAware, GeoService

@Component
public class GeoServiceImpl
extends AbstractGeoService

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

Author:

pavlidis

Field Summary

Fields inherited from class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService

arrayDesignService, persisterHelper

Constructor Summary

Constructors

Constructor

Description

GeoServiceImpl(ArrayDesignReportService arrayDesignReportService, BioAssayService bioAssayService, ExpressionExperimentReportService expressionExperimentReportService, ExpressionExperimentService expressionExperimentService, ExpressionExperimentPrePersistService expressionExperimentPrePersistService, TaxonService taxonService, CharacteristicService characteristicService, BioMaterialService bioMaterialSerivce, BibliographicReferenceService bibliographicReferenceService, AuditTrailService auditTrailService)

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 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	updateFromGEO(String geoAccession)	Refetch and reprocess the GEO series, updating select information.

Methods inherited from class ubic.gemma.core.loader.expression.geo.service.AbstractGeoService

getGeoDomainObjectGenerator, setBeanFactory, setGeoDomainObjectGenerator

Methods inherited from class java.lang.Object

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

Constructor Detail

GeoServiceImpl

@Autowired
public GeoServiceImpl(ArrayDesignReportService arrayDesignReportService,
                      BioAssayService bioAssayService,
                      ExpressionExperimentReportService expressionExperimentReportService,
                      ExpressionExperimentService expressionExperimentService,
                      ExpressionExperimentPrePersistService expressionExperimentPrePersistService,
                      TaxonService taxonService,
                      CharacteristicService characteristicService,
                      BioMaterialService bioMaterialSerivce,
                      BibliographicReferenceService bibliographicReferenceService,
                      AuditTrailService auditTrailService)

Method Detail

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.

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

Specified by:

fetchAndLoad in class AbstractGeoService

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

Specified by:

fetchAndLoad in class AbstractGeoService

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)

Description copied from interface: GeoService

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

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.

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.