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

Class AbstractSingleCellDetector

java.lang.Object

ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector

All Implemented Interfaces:

SingleCellDetector

Direct Known Subclasses:

AbstractSingleFileInSeriesSingleCellDetector, MexDetector

public abstract class AbstractSingleCellDetector
extends Object
implements SingleCellDetector

Field Summary

Fields

Modifier and Type	Field	Description
protected final org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Constructor	Description
AbstractSingleCellDetector()

Method Summary

Modifier and Type	Method	Description
protected boolean	existsAndHasExpectedSize(Path dest, String remoteFile, long expectedContentLength, boolean decompressIfNeeded, boolean storeCompressed)	Check if a file at a given destination exists and has the size of a remote file.
Path	getDownloadDirectory()
protected long	getSizeInBytes(String remoteFile)
protected InputStream	openSupplementaryFileAsStream(String filename, int attempt, boolean decompressIfNeeded)	Open a supplementary file as an input stream, possibly decompressing it.
protected <T> T	retry(SimpleRetryCallable<T,IOException> callable, String what)	Retry the given callable a certain number of times before giving up.
void	setDownloadDirectory(Path downloadDirectory)	Set the download directory to use for storing single-cell data.
void	setFTPClientFactory(FTPClientFactory ftpClientFactory)	Set the FTP client factory to use for downloading data over FTP.
void	setRetryPolicy(SimpleRetryPolicy retryPolicy)	Set the retry policy to use when downloading single-cell data.

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.expression.geo.singleCell.SingleCellDetector

downloadSingleCellData, downloadSingleCellData, getAdditionalSupplementaryFiles, getAdditionalSupplementaryFiles, getSingleCellDataLoader, hasSingleCellData, hasSingleCellData

Field Details

log

protected final org.apache.commons.logging.Log log

Constructor Details

AbstractSingleCellDetector

public AbstractSingleCellDetector()

Method Details

setFTPClientFactory

public void setFTPClientFactory(FTPClientFactory ftpClientFactory)

Set the FTP client factory to use for downloading data over FTP.

getDownloadDirectory

public Path getDownloadDirectory()

setDownloadDirectory

public void setDownloadDirectory(Path downloadDirectory)

Set the download directory to use for storing single-cell data.

It may be left unset if downloading is not intended or needed.

Specified by:

setDownloadDirectory in interface SingleCellDetector

setRetryPolicy

public void setRetryPolicy(SimpleRetryPolicy retryPolicy)

Description copied from interface: SingleCellDetector

Set the retry policy to use when downloading single-cell data.

Specified by:

setRetryPolicy in interface SingleCellDetector

retry

protected <T> T retry(SimpleRetryCallable<T,IOException> callable,
 String what)
               throws IOException

Retry the given callable a certain number of times before giving up.

Throws:

IOException

See Also:

• SimpleRetry

existsAndHasExpectedSize

protected boolean existsAndHasExpectedSize(Path dest,
 String remoteFile,
 long expectedContentLength,
 boolean decompressIfNeeded,
 boolean storeCompressed)
                                    throws IOException

Check if a file at a given destination exists and has the size of a remote file.

Parameters:

dest - file at destination

remoteFile - filename at origin

expectedContentLength - expected size, or -1 if unknown

decompressIfNeeded - if true and the remote file is gzipped, will only check if the local file exists

storeCompressed - if true and the remote file is *not* gzipped, will only check if the local file exists

Throws:

IOException

openSupplementaryFileAsStream

protected InputStream openSupplementaryFileAsStream(String filename,
 int attempt,
 boolean decompressIfNeeded)
                                             throws IOException

Open a supplementary file as an input stream, possibly decompressing it.

Throws:

IOException

getSizeInBytes

protected long getSizeInBytes(String remoteFile)
                       throws IOException

Throws:

IOException