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

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

Field Summary

Fields inherited from class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector

log

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

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

Methods inherited from class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector

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

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

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