Package ubic.gemma.core.loader.genome.taxon

Class TaxonFetcher

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.genome.taxon.TaxonFetcher

All Implemented Interfaces:

ArchiveFetcher, Fetcher

public class TaxonFetcher
extends FtpArchiveFetcher

Taxon information from NCBI comes as a tar.gz archive; only the names.dmp file is of interest. From ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

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
TaxonFetcher()

Method Summary

Modifier and Type	Method	Description
Collection<File>	fetch()	Fetch the Taxon bundle from NCBI.
protected String	formLocalFilePath(String unused, File newDir)
protected String	formRemoteFilePath(String identifier)
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, 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

Methods inherited from interface ubic.gemma.core.loader.util.fetcher.Fetcher

fetch

Constructor Detail

TaxonFetcher

public TaxonFetcher()

Method Detail

formRemoteFilePath

protected String formRemoteFilePath(String identifier)

Specified by:

formRemoteFilePath in class AbstractFetcher

initConfig

public void initConfig()

Specified by:

initConfig in class AbstractFetcher

fetch

public Collection<File> fetch()

Fetch the Taxon bundle from NCBI.

Returns:

local files

formLocalFilePath

protected String formLocalFilePath(String unused,
                                   File newDir)

Specified by:

formLocalFilePath in class AbstractFetcher

setNetDataSourceUtil

public void setNetDataSourceUtil()

Specified by:

setNetDataSourceUtil in class FtpFetcher