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 Fetcher	datasetFetcher
protected static org.apache.commons.logging.Log	log
protected GeoFamilyParser	parser
protected Fetcher	platformFetcher
protected Fetcher	seriesFetcher

Constructor Summary

Constructors

Constructor	Description
GeoDomainObjectGenerator()

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	initialize()	Initialize fetchers, clear out any data that was already generated by this Generator.
void	processDataSet(GeoSeries series, String dataSetAccession)	Process a data set and add it to the series
void	setDatasetFetcher(Fetcher df)
void	setDoSampleMatching(boolean doSampleMatching)
void	setPlatformFetcher(Fetcher platformFetcher)
void	setProcessPlatformsOnly(boolean b)
void	setSeriesFetcher(Fetcher seriesFetcher)

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

datasetFetcher

protected Fetcher datasetFetcher

seriesFetcher

protected Fetcher seriesFetcher

platformFetcher

protected Fetcher platformFetcher

parser

protected GeoFamilyParser parser

Constructor Detail

GeoDomainObjectGenerator

public GeoDomainObjectGenerator()

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

initialize

public void initialize()

Initialize fetchers, clear out any data that was already generated by this Generator.

processDataSet

public void processDataSet(GeoSeries series,
                           String dataSetAccession)

Process a data set and add it to the series

Parameters:

series - series

dataSetAccession - dataset accession

setDatasetFetcher

public void setDatasetFetcher(Fetcher df)

setDoSampleMatching

public void setDoSampleMatching(boolean doSampleMatching)

setPlatformFetcher

public void setPlatformFetcher(Fetcher platformFetcher)

Parameters:

platformFetcher - The platformFetcher to set.

setProcessPlatformsOnly

public void setProcessPlatformsOnly(boolean b)

setSeriesFetcher

public void setSeriesFetcher(Fetcher seriesFetcher)

Parameters:

seriesFetcher - The seriesFetcher to set.