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

Class GeoSingleCellDetector

java.lang.Object

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

All Implemented Interfaces:

AutoCloseable, ArchiveBasedSingleCellDetector, SeriesAwareSingleCellDetector, SingleCellDetector

public class GeoSingleCellDetector
extends Object
implements SingleCellDetector, ArchiveBasedSingleCellDetector, SeriesAwareSingleCellDetector, AutoCloseable

This is the main single-cell data detector that delegates to other more specific detectors.

Samples can be loaded in parallel when retrieving a GEO series with downloadSingleCellData(GeoSeries). The number of threads used is controlled by setNumberOfFetchThreads(int) and defaults to 4.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_NUMBER_OF_FETCH_THREADS	Default number of threads to use for fetching data.

Fields inherited from interface ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector

DEFAULT_MAX_ENTRY_SIZE_IN_ARCHIVE_TO_SKIP, DEFAULT_MAX_NUMBER_OF_ENTRIES_TO_SKIP

Constructor Summary

Constructors

Constructor	Description
GeoSingleCellDetector()

Method Summary

Modifier and Type	Method	Description
void	close()
Path	downloadSingleCellData(GeoSample sample)	Download single-cell data for the given GEO sample.
Path	downloadSingleCellData(GeoSample sample, SingleCellDataType dataType)
Path	downloadSingleCellData(GeoSeries series)	Download single-cell data from a GEO series to disk.
Path	downloadSingleCellData(GeoSeries series, GeoSample sample)	Download a sample in the context of a series.
Path	downloadSingleCellData(GeoSeries series, GeoSample sample, SingleCellDataType dataType)
void	downloadSingleCellData(GeoSeries series, SingleCellDataType dataType)
void	downloadSingleCellData(GeoSeries series, SingleCellDataType dataType, String supplementaryFile)
List<String>	getAdditionalSupplementaryFiles(GeoSample sample)	Obtain a list of all additional supplementary files.
List<String>	getAdditionalSupplementaryFiles(GeoSeries series)	Obtain a list of all additional supplementary files.
List<String>	getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
Set<SingleCellDataType>	getAllSingleCellDataTypes(GeoSeries series)	Obtain all single-cell data types a GEO series contains.
SingleCellDataLoader	getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)	Obtain a single-cell data loader.
SingleCellDataType	getSingleCellDataType(GeoSeries series)	Determine the type of single-cell data a GEO series contains.
boolean	hasSingleCellData(GeoSample sample)	Indicate if the given GEO sample has single-cell data.
boolean	hasSingleCellData(GeoSeries series)	Detects if a GEO series has single-cell data either at the series-level or in individual samples.
boolean	hasSingleCellData(GeoSeries series, GeoSample sample)
boolean	hasSingleCellDataInSeries(GeoSeries series)	Check if a GEO series has single-cell data at the series-level.
boolean	hasSingleCellDataInSeries(GeoSeries series, SingleCellDataType dataType)	Check if a GEO series has single-cell data at the series-level.
boolean	hasSingleCellDataInSra(GeoSample sample)	Check if a GEO sample has single-cell data in SRA.
boolean	hasSingleCellDataInSra(GeoSeries series)	Check if a GEO series has single-cell data in SRA.
boolean	hasSingleCellDataInSra(GeoSeries series, Collection<String> sraAccessions, Collection<String> sraAccessionsWithOtherDataTypes)
boolean	isSingleCell(GeoSample sample, boolean hasSingleCellDataInSeries)	Check if a GEO sample is single-cell by looking up its metadata.
boolean	isSingleNuclei(GeoSample sample, boolean hasSingleCellDataInSeries)	Check if a GEO sample is single-nuclei by looking up its metadata.
void	resetMexFileSuffixes()
void	setCellRangerPrefix(Path cellRangerPrefix)
void	setDownloadDirectory(Path dir)	Directory where single-cell data is downloaded.
void	setFTPClientFactory(FTPClientFactory factory)	Set the FTPClient factory used to create FTP connection to retrieve supplementary materials.
void	setMaxEntrySizeInArchiveToSkip(long maxNumberOfEntriesToSkip)	Set the maximum size of an archive entry to skip the supplementary file altogether.
void	setMaxNumberOfEntriesToSkip(long maxNumberOfEntriesToSkip)	Set the maximum number of archive entries to skip in order to ignore the supplementary file altogether.
void	setMexFileSuffixes(String barcodes, String features, String matrix)	Set the suffixes to use to detect MEX metadata.
void	setNumberOfFetchThreads(int numberOfFetchThreads)	Number of threads to use for downloading single-cell data.
void	setRetryPolicy(SimpleRetryPolicy retryPolicy)	Set the retry policy to use when downloading single-cell data.
void	setSraFetcher(SraFetcher sraFetcher)	Set the SraFetcher used to fetch SRA metadata.

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_NUMBER_OF_FETCH_THREADS

public static final int DEFAULT_NUMBER_OF_FETCH_THREADS

Default number of threads to use for fetching data.

See Also:

• Constant Field Values

Constructor Details

GeoSingleCellDetector

public GeoSingleCellDetector()

Method Details

close

public void close()

Specified by:

close in interface AutoCloseable

setNumberOfFetchThreads

public void setNumberOfFetchThreads(int numberOfFetchThreads)

Number of threads to use for downloading single-cell data.

setFTPClientFactory

public void setFTPClientFactory(FTPClientFactory factory)

Set the FTPClient factory used to create FTP connection to retrieve supplementary materials.

setDownloadDirectory

public void setDownloadDirectory(Path dir)

Directory where single-cell data is downloaded.

Data are organized by GEO series or GEO series accessions.

For AnnData, Seurat Disk and Loom:

• {downloadDir}/{geoSeriesAccession}.h5ad
• {downloadDir}/{geoSeriesAccession}.h5Seurat
• {downloadDir}/{geoSeriesAccession}.loom

MEX data is organized in a subdirectory named after the GEO series accession:

• {downloadDir}/{geoSampleAccession}/barcodes.tsv.gz
• {downloadDir}/{geoSampleAccession}/features.tsv.gz
• {downloadDir}/{geoSampleAccession}/matrix.mtx.gz

Downloading Loom at the sample-level is not supported yet.

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

setMexFileSuffixes

public void setMexFileSuffixes(String barcodes,
 String features,
 String matrix)

Set the suffixes to use to detect MEX metadata.

resetMexFileSuffixes

public void resetMexFileSuffixes()

setMaxEntrySizeInArchiveToSkip

public void setMaxEntrySizeInArchiveToSkip(long maxNumberOfEntriesToSkip)

Description copied from interface: ArchiveBasedSingleCellDetector

Set the maximum size of an archive entry to skip the supplementary file altogether.

Use -1 to indicate no limit.

Note that if a relevant file was previously found in the archive, it will not be skipped.

Specified by:

setMaxEntrySizeInArchiveToSkip in interface ArchiveBasedSingleCellDetector

setMaxNumberOfEntriesToSkip

public void setMaxNumberOfEntriesToSkip(long maxNumberOfEntriesToSkip)

Description copied from interface: ArchiveBasedSingleCellDetector

Set the maximum number of archive entries to skip in order to ignore the supplementary file altogether.

Use -1 to indicate no limit.

Note that if a relevant file was previously found in the archive, it will not be ignored.

Specified by:

setMaxNumberOfEntriesToSkip in interface ArchiveBasedSingleCellDetector

setSraFetcher

public void setSraFetcher(@Nullable
 SraFetcher sraFetcher)

Set the SraFetcher used to fetch SRA metadata.

setCellRangerPrefix

public void setCellRangerPrefix(Path cellRangerPrefix)

hasSingleCellData

public boolean hasSingleCellData(GeoSeries series)

Detects if a GEO series has single-cell data either at the series-level or in individual samples.

Specified by:

hasSingleCellData in interface SingleCellDetector

hasSingleCellData

public boolean hasSingleCellData(GeoSample sample)

Description copied from interface: SingleCellDetector

Indicate if the given GEO sample has single-cell data.

Specified by:

hasSingleCellData in interface SingleCellDetector

hasSingleCellData

public boolean hasSingleCellData(GeoSeries series,
 GeoSample sample)

Specified by:

hasSingleCellData in interface SeriesAwareSingleCellDetector

getSingleCellDataType

public SingleCellDataType getSingleCellDataType(GeoSeries series)
                                         throws NoSingleCellDataFoundException

Determine the type of single-cell data a GEO series contains.

Throws:

NoSingleCellDataFoundException

getAllSingleCellDataTypes

public Set<SingleCellDataType> getAllSingleCellDataTypes(GeoSeries series)

Obtain all single-cell data types a GEO series contains.

downloadSingleCellData

public Path downloadSingleCellData(GeoSeries series)
                            throws NoSingleCellDataFoundException,
IOException

Download single-cell data from a GEO series to disk.

This has to be done prior to

invalid reference

#getSingleCellDataLoader(GeoSeries)

.

Specified by:

downloadSingleCellData in interface SingleCellDetector

Returns:

a directory or file containing the downloaded series data

Throws:

NoSingleCellDataFoundException - if no single-cell data is found either at the series level or in individual samples

UnsupportedOperationException - if single-cell data is found at the series level

IOException

downloadSingleCellData

public void downloadSingleCellData(GeoSeries series,
 SingleCellDataType dataType,
 String supplementaryFile)
                            throws IOException

Throws:

IOException

downloadSingleCellData

public void downloadSingleCellData(GeoSeries series,
 SingleCellDataType dataType)
                            throws NoSingleCellDataFoundException,
IOException

Throws:

NoSingleCellDataFoundException

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSeries series,
 GeoSample sample)
                            throws NoSingleCellDataFoundException,
IOException

Download a sample in the context of a series.

This is only applicable to MEX and Loom.

Specified by:

downloadSingleCellData in interface SeriesAwareSingleCellDetector

Throws:

NoSingleCellDataFoundException

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSeries series,
 GeoSample sample,
 SingleCellDataType dataType)
                            throws NoSingleCellDataFoundException,
IOException

Throws:

NoSingleCellDataFoundException

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSample sample)
                            throws NoSingleCellDataFoundException,
IOException

Description copied from interface: SingleCellDetector

Download single-cell data for the given GEO sample.

Specified by:

downloadSingleCellData in interface SingleCellDetector

Returns:

a directory or file containing the downloaded sample data

Throws:

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

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSample sample,
 SingleCellDataType dataType)
                            throws NoSingleCellDataFoundException,
IOException

Throws:

NoSingleCellDataFoundException

IOException

getSingleCellDataLoader

public SingleCellDataLoader getSingleCellDataLoader(GeoSeries series,
 SingleCellDataLoaderConfig config)
                                             throws NoSingleCellDataFoundException

Obtain a single-cell data loader.

Only local files previously retrieved with downloadSingleCellData(GeoSeries) are inspected.

Specified by:

getSingleCellDataLoader in interface SingleCellDetector

Throws:

NoSingleCellDataFoundException - if no single-cell data was found on-disk

UnsupportedOperationException - if single-cell data was found, but cannot be loaded

getAdditionalSupplementaryFiles

public List<String> getAdditionalSupplementaryFiles(GeoSeries series)

Description copied from interface: SingleCellDetector

Obtain a list of all additional supplementary files.

Specified by:

getAdditionalSupplementaryFiles in interface SingleCellDetector

getAdditionalSupplementaryFiles

public List<String> getAdditionalSupplementaryFiles(GeoSeries series,
 GeoSample sample)

Specified by:

getAdditionalSupplementaryFiles in interface SeriesAwareSingleCellDetector

getAdditionalSupplementaryFiles

public List<String> getAdditionalSupplementaryFiles(GeoSample sample)

Description copied from interface: SingleCellDetector

Obtain a list of all additional supplementary files.

Specified by:

getAdditionalSupplementaryFiles in interface SingleCellDetector

hasSingleCellDataInSeries

public boolean hasSingleCellDataInSeries(GeoSeries series)

Check if a GEO series has single-cell data at the series-level.

hasSingleCellDataInSeries

public boolean hasSingleCellDataInSeries(GeoSeries series,
 SingleCellDataType dataType)

Check if a GEO series has single-cell data at the series-level.

hasSingleCellDataInSra

public boolean hasSingleCellDataInSra(GeoSeries series)

Check if a GEO series has single-cell data in SRA.

hasSingleCellDataInSra

public boolean hasSingleCellDataInSra(GeoSeries series,
 Collection<String> sraAccessions,
 Collection<String> sraAccessionsWithOtherDataTypes)

hasSingleCellDataInSra

public boolean hasSingleCellDataInSra(GeoSample sample)

Check if a GEO sample has single-cell data in SRA.

isSingleCell

public boolean isSingleCell(GeoSample sample,
 boolean hasSingleCellDataInSeries)

Check if a GEO sample is single-cell by looking up its metadata.

Parameters:

hasSingleCellDataInSeries - indicate if the series has single-cell data, this is used as a last resort to determine if a given sample is single-cell, use hasSingleCellDataInSeries(GeoSeries) to compute and reuse this value.

isSingleNuclei

public boolean isSingleNuclei(GeoSample sample,
 boolean hasSingleCellDataInSeries)

Check if a GEO sample is single-nuclei by looking up its metadata.