AbstractSingleH5FileInSeriesSingleCellDetector (Gemma 1.32.0 API)

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

All Methods Instance Methods Concrete Methods
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 Detail

AbstractSingleH5FileInSeriesSingleCellDetector

protected AbstractSingleH5FileInSeriesSingleCellDetector(String name,
                                                         String extension)

Method Detail
- 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