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

Class AbstractGeoService

java.lang.Object

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

All Implemented Interfaces:

Aware, BeanFactoryAware, GeoService

Direct Known Subclasses:

GeoServiceImpl

public abstract class AbstractGeoService
extends Object
implements BeanFactoryAware, GeoService

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected ArrayDesignService	arrayDesignService
protected PersisterHelper	persisterHelper

Constructor Summary

Constructors

Constructor	Description
AbstractGeoService()

Method Summary

Modifier and Type	Method	Description
abstract Collection<?>	fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform)	Load data, no restrictions on superseries or subseries
abstract Collection<?>	fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform, boolean allowSuperSeriesImport, boolean allowSubSeriesImport)
GeoDomainObjectGenerator	getGeoDomainObjectGenerator()	This is supplied to allow clients to check that the generator has been set correctly.
void	setBeanFactory(BeanFactory beanFactory)
void	setGeoDomainObjectGenerator(GeoDomainObjectGenerator generator)

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.expression.geo.service.GeoService

addElements, loadFromSoftFile, updateFromGEO

Field Detail

persisterHelper

@Autowired
protected PersisterHelper persisterHelper

arrayDesignService

@Autowired
protected ArrayDesignService arrayDesignService

Constructor Detail

AbstractGeoService

public AbstractGeoService()

Method Detail

fetchAndLoad

public abstract 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

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

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

getGeoDomainObjectGenerator

public GeoDomainObjectGenerator getGeoDomainObjectGenerator()

Description copied from interface: GeoService

This is supplied to allow clients to check that the generator has been set correctly.

Specified by:

getGeoDomainObjectGenerator in interface GeoService

Returns:

generator

setGeoDomainObjectGenerator

public void setGeoDomainObjectGenerator(GeoDomainObjectGenerator generator)

Specified by:

setGeoDomainObjectGenerator in interface GeoService

setBeanFactory

public void setBeanFactory(BeanFactory beanFactory)
                    throws BeansException

Specified by:

setBeanFactory in interface BeanFactoryAware

Throws:

BeansException