Package ubic.gemma.core.loader.expression.arrayExpress

Class DataFileFetcher

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.arrayExpress.DataFileFetcher

All Implemented Interfaces:

ArchiveFetcher, Fetcher

public class DataFileFetcher
extends FtpArchiveFetcher

ArrayExpress stores files in an FTP site as tarred-gzipped archives. Each tar file contains the MAGE file and the datacube external files. This class can download an experiment, unpack the tar file, and put the resulting files onto a local filesystem.

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
DataFileFetcher()

Method Summary

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

DataFileFetcher

public DataFileFetcher()

Method Details

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 - identifier

Returns:

local files

formLocalFilePath

public String formLocalFilePath(String identifier,
 File newDir)

Specified by:

formLocalFilePath in class AbstractFetcher

formRemoteFilePath

public String formRemoteFilePath(String identifier)

Specified by:

formRemoteFilePath in class AbstractFetcher

Parameters:

identifier - - e.g. E-MEXP-955

Returns:

remote file path

getMageMlFile

public File getMageMlFile(Collection<File> files)

initConfig

public void initConfig()

Specified by:

initConfig in class AbstractFetcher

setNetDataSourceUtil

public void setNetDataSourceUtil()

Specified by:

setNetDataSourceUtil in class FtpFetcher