DataFileFetcher (Gemma 1.31.13 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.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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Collection<LocalFile>`	`fetch(String identifier)`	Fetch files according to the identifier provided.
`String`	`formLocalFilePath(String identifier, File newDir)`
`String`	`formRemoteFilePath(String identifier)`
`LocalFile`	`getMageMlFile(Collection<LocalFile> 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 Detail
  - DataFileFetcher
```
public DataFileFetcher()
```
- Method Detail
  - fetch
```
public Collection<LocalFile> 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 LocalFile getMageMlFile(Collection<LocalFile> files)
```
  - initConfig
```
public void initConfig()
```
    Specified by:
    
    initConfig in class AbstractFetcher
  - setNetDataSourceUtil
```
public void setNetDataSourceUtil()
```
    Specified by:
    
    setNetDataSourceUtil in class FtpFetcher