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

Class RawDataFetcher

java.lang.Object

ubic.gemma.core.loader.util.fetcher.AbstractFetcher

ubic.gemma.core.loader.util.fetcher.FtpFetcher

ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher

ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher

All Implemented Interfaces:

ArchiveFetcher, Fetcher

public class RawDataFetcher
extends FtpArchiveFetcher

Retrieve and unpack the raw data files for GEO series. These are the CEL and other files (RPT, EXP and maybe DAT) for Affymetrix data sets. For other types of arrays there may also be raw data?

Author:

pavlidis

Field Summary

Fields inherited from class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher

doDelete, expander

Fields inherited from class ubic.gemma.core.loader.util.fetcher.FtpFetcher

avoidDownload, ftpClient, netDataSourceUtil

Fields inherited from class ubic.gemma.core.loader.util.fetcher.AbstractFetcher

allowUseExisting, force, INFO_UPDATE_INTERVAL, localBasePath, log, remoteBaseDir

Constructor Summary

Constructors

Constructor	Description
RawDataFetcher()

Method Summary

Modifier and Type	Method	Description
boolean	checkForFile(String identifier)
Collection<File>	fetch(String identifier)	Fetch files according to the identifier provided.
protected String	formLocalFilePath(String identifier, File newDir)
protected String	formRemoteFilePath(String identifier)
void	initConfig()
final void	setNetDataSourceUtil()

Methods inherited from class ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher

cleanUp, doTask, initArchiveHandler, listFiles, setDeleteAfterUnpack, setExcludePattern, setForce, unPack

Methods inherited from class ubic.gemma.core.loader.util.fetcher.FtpFetcher

defineTask, fetch, getExpectedSize, getNetDataSourceUtil, setAvoidDownload

Methods inherited from class ubic.gemma.core.loader.util.fetcher.AbstractFetcher

fetchedFile, fetchedFile, getExistingFile, getLocalBasePath, isForce, mkdir, mkdir, setAllowUseExisting, waitForDownload

Methods inherited from class java.lang.Object

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

Constructor Details

RawDataFetcher

public RawDataFetcher()

Method Details

checkForFile

public boolean checkForFile(String identifier)

fetch

public Collection<File> fetch(String identifier)

Description copied from interface: Fetcher

Fetch files according to the identifier provided.

Specified by:

fetch in interface Fetcher

Overrides:

fetch in class FtpFetcher

Parameters:

identifier - The url for the supplementary file.

Returns:

local files

setNetDataSourceUtil

public final void setNetDataSourceUtil()

Specified by:

setNetDataSourceUtil in class FtpFetcher

formLocalFilePath

protected String formLocalFilePath(String identifier,
 File newDir)

Specified by:

formLocalFilePath in class AbstractFetcher

formRemoteFilePath

protected String formRemoteFilePath(String identifier)

Specified by:

formRemoteFilePath in class AbstractFetcher

initConfig

public void initConfig()

Specified by:

initConfig in class AbstractFetcher