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

Class GeoBrowserServiceImpl

java.lang.Object

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

All Implemented Interfaces:

DisposableBean, InitializingBean, GeoBrowserService

@Lazy
@Component
public class GeoBrowserServiceImpl
extends Object
implements GeoBrowserService, InitializingBean, DisposableBean

This is marked as Lazy since we don't use it outside Gemma Web, so it won't be loaded unless it's needed.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected ArrayDesignService	arrayDesignService
protected ExpressionExperimentService	expressionExperimentService

Constructor Summary

Constructors

Constructor	Description
GeoBrowserServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
void	destroy()
String	getDetails(String accession, String contextPath)	Get details from GEO about an accession.
List<GeoRecord>	getRecentGeoRecords(int start, int count)
List<GeoRecord>	searchGeoRecords(String searchString, int start, int count, boolean detailed)
boolean	toggleUsability(String accession)

Methods inherited from class java.lang.Object

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

Field Detail

expressionExperimentService

@Autowired
protected ExpressionExperimentService expressionExperimentService

arrayDesignService

@Autowired
protected ArrayDesignService arrayDesignService

Constructor Detail

GeoBrowserServiceImpl

public GeoBrowserServiceImpl()

Method Detail

afterPropertiesSet

public void afterPropertiesSet()
                        throws XPathExpressionException

Specified by:

afterPropertiesSet in interface InitializingBean

Throws:

XPathExpressionException

destroy

public void destroy()
             throws Exception

Specified by:

destroy in interface DisposableBean

Throws:

Exception

getDetails

public String getDetails(String accession,
                         String contextPath)
                  throws IOException

Description copied from interface: GeoBrowserService

Get details from GEO about an accession.

Specified by:

getDetails in interface GeoBrowserService

Parameters:

accession - accession

Returns:

details

Throws:

IOException - if there is a problem while manipulating the file

getRecentGeoRecords

public List<GeoRecord> getRecentGeoRecords(int start,
                                           int count)
                                    throws IOException,
                                           ParseException

Specified by:

getRecentGeoRecords in interface GeoBrowserService

Parameters:

start - page number, not starting record

count - page size

Returns:

geo records

Throws:

IOException - if there is a problem while manipulating the file

ParseException - if there is a problem with parsing

searchGeoRecords

public List<GeoRecord> searchGeoRecords(String searchString,
                                        int start,
                                        int count,
                                        boolean detailed)
                                 throws IOException

Specified by:

searchGeoRecords in interface GeoBrowserService

Parameters:

searchString - can be null

start - first record to retrieve

count - how many records to retrieve

detailed - if true, more information is retrieved (slow)

Returns:

collection of GeoRecords

Throws:

IOException

toggleUsability

public boolean toggleUsability(String accession)

Specified by:

toggleUsability in interface GeoBrowserService