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

Class AbstractSingleFileInSeriesSingleCellDetector

java.lang.Object

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

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

All Implemented Interfaces:

SingleCellDetector

Direct Known Subclasses:

AbstractSingleH5FileInSeriesSingleCellDetector, LoomSingleCellDetector

public abstract class AbstractSingleFileInSeriesSingleCellDetector
extends AbstractSingleCellDetector

Handle detection and download of single-cell data from a single file in the supplementary materials of a GEO series.

Author:

poirigui

Field Summary

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

log

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected boolean	accepts(String supplementaryFile)	Indicate if the given supplementary file is accepted.
Path	downloadSingleCellData(GeoSample sample)	Download single-cell data for the given GEO sample.
Path	downloadSingleCellData(GeoSeries series)	Download single-cell data for the given GEO series.
Path	downloadSingleCellData(GeoSeries series, String file)	Download a specific supplementary file at the series-level.
List<String>	getAdditionalSupplementaryFiles(GeoSample sample)	Obtain a list of all additional supplementary files.
List<String>	getAdditionalSupplementaryFiles(GeoSeries sample)	Obtain a list of all additional supplementary files.
protected Path	getDest(GeoSeries series)	Obtain the download destination for the single-cell data file.
boolean	hasSingleCellData(GeoSample sample)	Detection is not supported at the sample level.
boolean	hasSingleCellData(GeoSeries series)	Indicate if the given GEO series has single cell data.

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

existsAndHasExpectedSize, 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

AbstractSingleFileInSeriesSingleCellDetector

protected AbstractSingleFileInSeriesSingleCellDetector(String name,
                                                       String extension)

Method Detail

accepts

protected boolean accepts(String supplementaryFile)

Indicate if the given supplementary file is accepted.

The default implementation checks if the file ends with the extension (or the extension + .gz).

getDest

protected Path getDest(GeoSeries series)

Obtain the download destination for the single-cell data file.

hasSingleCellData

public boolean hasSingleCellData(GeoSeries series)

Description copied from interface: SingleCellDetector

Indicate if the given GEO series has single cell data.

hasSingleCellData

public boolean hasSingleCellData(GeoSample sample)

Detection is not supported at the sample level.

downloadSingleCellData

public Path downloadSingleCellData(GeoSeries series)
                            throws NoSingleCellDataFoundException,
                                   IOException

Download single-cell data for the given GEO series.

Returns:

a directory or file containing the downloaded series data

Throws:

IllegalArgumentException - if more than one matching file is present in the supplementary files of the series, use downloadSingleCellData(GeoSeries, String) as a workaround.

NoSingleCellDataFoundException - if there is no single cell data for the given series

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSeries series,
                                   String file)
                            throws IOException

Download a specific supplementary file at the series-level.

Throws:

IllegalArgumentException - if the supplementary file is not present in the series

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSample sample)
                            throws NoSingleCellDataFoundException

Description copied from interface: SingleCellDetector

Download single-cell data for the given GEO sample.

Returns:

a directory or file containing the downloaded sample data

Throws:

NoSingleCellDataFoundException - if there is no single cell data for the given sample

getAdditionalSupplementaryFiles

public List<String> getAdditionalSupplementaryFiles(GeoSeries sample)

Description copied from interface: SingleCellDetector

Obtain a list of all additional supplementary files.

getAdditionalSupplementaryFiles

public List<String> getAdditionalSupplementaryFiles(GeoSample sample)

Description copied from interface: SingleCellDetector

Obtain a list of all additional supplementary files.