TaxonFetcher (Gemma 1.31.4 API)

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Collection<LocalFile>`	`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, 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<LocalFile> 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