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

Class MexDetector

java.lang.Object

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

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

All Implemented Interfaces:

ArchiveBasedSingleCellDetector, SeriesAwareSingleCellDetector, SingleCellDetector

public class MexDetector
extends AbstractSingleCellDetector
implements ArchiveBasedSingleCellDetector, SeriesAwareSingleCellDetector

Detects MEX data from GEO series and samples.

This detector is not specific to 10x MEX data since MEX itself is a widely used format in single-cell studies. Logic specific to 10x are stored in TenXCellRangerUtils.

Older 10x MEX datasets use the genes.tsv.gz instead of features.tsv.gz. Those are copied using the new naming scheme into the download directory.

MEX data is only supported at the sample-level. However, we do support detecting its presence at the series-level, but not downloading.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DEFAULT_BARCODE_METADATA_FILE_SUFFIX
static final String	DEFAULT_BARCODES_FILE_SUFFIX
static final String	DEFAULT_FEATURES_FILE_SUFFIX
static final String	DEFAULT_GENES_FILE_SUFFIX
static final String	DEFAULT_MATRIX_FILE_SUFFIX

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

log

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
MexDetector()

Method Summary

Modifier and Type	Method	Description
Path	downloadSingleCellData(GeoSample sample)	Retrieve single-cell data for the given GEO sample to disk.
Path	downloadSingleCellData(GeoSeries series)	Download single-cell data for the given GEO series.
Path	downloadSingleCellData(GeoSeries series, GeoSample sample)	Download a GEO sample within the context of its series.
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)
SingleCellDataLoader	getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)	Obtain a single cell data loader for the given GEO series based on previously downloading data.
boolean	hasSingleCellData(GeoSample sample)	Indicate if the given GEO sample has single-cell data.
boolean	hasSingleCellData(GeoSample sample, boolean allowArchiveLookup)	Check if a GEO sample contains single-cell data.
boolean	hasSingleCellData(GeoSeries series)	Indicate if the given GEO series has single-cell data.
boolean	hasSingleCellData(GeoSeries series, GeoSample sample)	Check if a sample contains single-cell data in the context of its series.
void	setBarcodeMetadataFileSuffix(String barcodeMetadataFileSuffix)
void	setBarcodesFileSuffix(String barcodesFileSuffix)
void	setCellRangerPrefix(Path cellRangerPrefix)
void	setFeaturesFileSuffix(String featuresFileSuffix)
void	setGenesFileSuffix(String genesFileSuffix)
void	setMatrixFileSuffix(String matrixFileSuffix)
void	setMaxEntrySizeInArchiveToSkip(long maxEntrySizeInArchiveToSkip)	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.

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

setDownloadDirectory, setRetryPolicy

Field Details

DEFAULT_BARCODES_FILE_SUFFIX

public static final String DEFAULT_BARCODES_FILE_SUFFIX

See Also:

• Constant Field Values

DEFAULT_BARCODE_METADATA_FILE_SUFFIX

public static final String DEFAULT_BARCODE_METADATA_FILE_SUFFIX

See Also:

• Constant Field Values

DEFAULT_FEATURES_FILE_SUFFIX

public static final String DEFAULT_FEATURES_FILE_SUFFIX

See Also:

• Constant Field Values

DEFAULT_GENES_FILE_SUFFIX

public static final String DEFAULT_GENES_FILE_SUFFIX

See Also:

• Constant Field Values

DEFAULT_MATRIX_FILE_SUFFIX

public static final String DEFAULT_MATRIX_FILE_SUFFIX

See Also:

• Constant Field Values

Constructor Details

MexDetector

public MexDetector()

Method Details

setMaxEntrySizeInArchiveToSkip

public void setMaxEntrySizeInArchiveToSkip(long maxEntrySizeInArchiveToSkip)

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

hasSingleCellData

public boolean hasSingleCellData(GeoSeries series)

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

MEX data detection is not supported at the series level, so while this method can return true if barcodes/genes/matrices are present in the series supplementary files, downloadSingleCellData(GeoSeries) will subsequently fail.

Specified by:

hasSingleCellData in interface SingleCellDetector

hasSingleCellData

public boolean hasSingleCellData(GeoSeries series,
 GeoSample sample)

Check if a sample contains single-cell data in the context of its series.

Specified by:

hasSingleCellData in interface SeriesAwareSingleCellDetector

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(GeoSample sample,
 boolean allowArchiveLookup)

Check if a GEO sample contains single-cell data.

Parameters:

allowArchiveLookup - allow looking into archives for MEX files

downloadSingleCellData

public Path downloadSingleCellData(GeoSeries series)
                            throws NoSingleCellDataFoundException

Description copied from interface: SingleCellDetector

Download single-cell data for the given GEO series.

Specified by:

downloadSingleCellData in interface SingleCellDetector

Returns:

a directory or file containing the downloaded series data

Throws:

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

downloadSingleCellData

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

Download a GEO sample within the context of its series.

This will first download the sample with downloadSingleCellData(String, Collection) with the merged supplementary files from the series and the sample, then create a series/sample folder structure and finally hard-link all the sample files in there. This ensures that if two series mention the same sample, they can reuse the same files.

Specified by:

downloadSingleCellData in interface SeriesAwareSingleCellDetector

Throws:

NoSingleCellDataFoundException

IOException

downloadSingleCellData

public Path downloadSingleCellData(GeoSample sample)
                            throws NoSingleCellDataFoundException,
IOException

Retrieve single-cell data for the given GEO sample to disk.

Specified by:

downloadSingleCellData in interface SingleCellDetector

Returns:

a directory or file containing the downloaded sample data

Throws:

NoSingleCellDataFoundException - if no single-cell data is found in the given GEO sample

IOException

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(GeoSample sample)

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

getSingleCellDataLoader

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

Description copied from interface: SingleCellDetector

Obtain a single cell data loader for the given GEO series based on previously downloading data.

Specified by:

getSingleCellDataLoader in interface SingleCellDetector

Throws:

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

setBarcodesFileSuffix

public void setBarcodesFileSuffix(String barcodesFileSuffix)

setBarcodeMetadataFileSuffix

public void setBarcodeMetadataFileSuffix(@Nullable
 String barcodeMetadataFileSuffix)

setFeaturesFileSuffix

public void setFeaturesFileSuffix(String featuresFileSuffix)

setGenesFileSuffix

public void setGenesFileSuffix(@Nullable
 String genesFileSuffix)

setMatrixFileSuffix

public void setMatrixFileSuffix(String matrixFileSuffix)

setCellRangerPrefix

public void setCellRangerPrefix(@Nullable
 Path cellRangerPrefix)