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

Class GeoDomainObjectGenerator

java.lang.Object

ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator

All Implemented Interfaces:

SourceDomainObjectGenerator

Direct Known Subclasses:

GeoDomainObjectGeneratorLocal

public class GeoDomainObjectGenerator
extends Object
implements SourceDomainObjectGenerator

Handle fetching and parsing GEO files.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected static org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Modifier	Constructor	Description
	GeoDomainObjectGenerator()
protected	GeoDomainObjectGenerator(DatasetFetcher datasetFetcher, SeriesFetcher seriesFetcher, Fetcher platformFetcher)

Method Summary

Modifier and Type	Method	Description
Collection<? extends GeoData>	generate(String geoAccession)	Combines the necessary data fetching and parsing steps to get a collection of source domain objects.
Collection<DatabaseEntry>	getProjectedAccessions(String geoAccession)	Determine the set of external accession values that will be generated during parsing.
void	processDataSet(GeoSeries series, String dataSetAccession, GeoFamilyParser parser)	Process a data set and add it to the series
void	setDoSampleMatching(boolean doSampleMatching)
void	setNcbiApiKey(String ncbiApiKey)	Set the NCBI API key to use.
void	setProcessPlatformsOnly(boolean b)

Methods inherited from class java.lang.Object

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

Field Detail

log

protected static org.apache.commons.logging.Log log

Constructor Detail

GeoDomainObjectGenerator

public GeoDomainObjectGenerator()

GeoDomainObjectGenerator

protected GeoDomainObjectGenerator(DatasetFetcher datasetFetcher,
                                   SeriesFetcher seriesFetcher,
                                   Fetcher platformFetcher)

Method Detail

generate

public Collection<? extends GeoData> generate(String geoAccession)

Description copied from interface: SourceDomainObjectGenerator

Combines the necessary data fetching and parsing steps to get a collection of source domain objects.

Specified by:

generate in interface SourceDomainObjectGenerator

Parameters:

geoAccession - , either a GPL, GDS or GSE value.

Returns:

If processPlatformsOnly is true, a collection of GeoPlatforms. Otherwise a Collection of series (just one). If the accession is a GPL then processPlatformsOnly is set to true and any sample data is ignored.

getProjectedAccessions

public Collection<DatabaseEntry> getProjectedAccessions(String geoAccession)

Determine the set of external accession values that will be generated during parsing. This can be used to pre-empty time-consuming fetch and download of data we already have.

Parameters:

geoAccession - geo accession

Returns:

database entries

processDataSet

public void processDataSet(GeoSeries series,
                           String dataSetAccession,
                           GeoFamilyParser parser)

Process a data set and add it to the series

setNcbiApiKey

public void setNcbiApiKey(String ncbiApiKey)

Set the NCBI API key to use.

This is only used to resolve GEO datasets from series, so it is not critical for the good functioning of this class, but it is preferable to set it.

setDoSampleMatching

public void setDoSampleMatching(boolean doSampleMatching)

setProcessPlatformsOnly

public void setProcessPlatformsOnly(boolean b)