Class AbstractSingleH5FileInSeriesSingleCellDetector

java.lang.Object

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

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

ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector

All Implemented Interfaces:

SingleCellDetector

Direct Known Subclasses:

AnnDataDetector, SeuratDiskDetector

public abstract class AbstractSingleH5FileInSeriesSingleCellDetector
extends AbstractSingleFileInSeriesSingleCellDetector

Author:

poirigui

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractSingleH5FileInSeriesSingleCellDetector(String name, String extension)

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.
protected boolean	isTruncated(Path dest)

Methods inherited from class AbstractSingleFileInSeriesSingleCellDetector

accepts, downloadSingleCellData, downloadSingleCellData, downloadSingleCellData, getAdditionalSupplementaryFiles, getAdditionalSupplementaryFiles, getDest, hasSingleCellData, hasSingleCellData

Methods inherited from class AbstractSingleCellDetector

getDownloadDirectory, getProgressReporterFactory, getSizeInBytes, openSupplementaryFileAsStream, retry, setDownloadDirectory, setFTPClientFactory, setProgressReporterFactory, setRetryPolicy

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface SingleCellDetector

getSingleCellDataLoader

Constructor Details

AbstractSingleH5FileInSeriesSingleCellDetector

protected AbstractSingleH5FileInSeriesSingleCellDetector(String name,
 String extension)

Method Details

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.

In addition to size and existence, also check if the H5 is truncated.

Overrides:

existsAndHasExpectedSize in class AbstractSingleCellDetector

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

isTruncated

protected boolean isTruncated(Path dest)
                       throws IOException

Throws:

IOException