Class MexSingleCellDataLoaderTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderTest

@ContextConfiguration
@ExtendWith(NetworkAvailableExtension.class)
public class MexSingleCellDataLoaderTest
extends BaseTest5

Constructor Summary

Constructors

Constructor	Description
MexSingleCellDataLoaderTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	testEmpty()
void	testGSE125708(Path tempDownloadDir)	This GEO series includes cell types in the barcodes.tsv.gz files.
void	testGSE125708OverTheWire()	Truth-source variant of testGSE125708(Path).
void	testGSE141552(Path tempDownloadDir)	This dataset does not filter empty droplets and thus many barcodes are simply unused and can be discarded.
void	testGSE141552OverTheWire()	Truth-source variant of testGSE141552(Path).
void	testGSE224438()
void	testLoadSpecificSamples()
void	testUnmatchedSample()

Methods inherited from class Object

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

Constructor Details

MexSingleCellDataLoaderTest

public MexSingleCellDataLoaderTest()

Method Details

setUp

@BeforeEach
public void setUp()
           throws IOException

Throws:

IOException

testEmpty

@Test
public void testEmpty()
               throws IOException

Throws:

IOException

testGSE224438

@Test
@Tag("slow")
public void testGSE224438()
                   throws IOException

Throws:

IOException

testLoadSpecificSamples

@Test
public void testLoadSpecificSamples()
                             throws IOException

Throws:

IOException

testUnmatchedSample

@Test
public void testUnmatchedSample()
                         throws IOException

Throws:

IOException

testGSE141552

@Test
@Tag("integration")
public void testGSE141552(@TempDir
 Path tempDownloadDir)
                   throws IOException,
NoSingleCellDataFoundException

This dataset does not filter empty droplets and thus many barcodes are simply unused and can be discarded.

Uses a chopped MEX fixture from the classpath (50 000 barcodes x ~1000 features per sample) so the loader is exercised end-to-end without a real GEO download. See GSE141552-chopped/README.md for regeneration. The over-the-wire variant is testGSE141552OverTheWire().

Throws:

IOException

NoSingleCellDataFoundException

testGSE141552OverTheWire

@Test
@Tag("slow") @Tag("network") @Tag("integration") @Tag("geo")
@NetworkAvailable(url="ftp://ftp.ncbi.nlm.nih.gov/geo/series/")
public void testGSE141552OverTheWire()
                              throws IOException,
NoSingleCellDataFoundException

Truth-source variant of testGSE141552(Path). Downloads the full ~50-200 MB GSE141552 bundle from NCBI FTP at test time and asserts against the upstream cell / barcode / vector counts. Kept as a regression guard so that the chopped fixture's faithfulness can be re-verified on demand.

Throws:

IOException

NoSingleCellDataFoundException

testGSE125708

@Test
@Tag("integration")
public void testGSE125708(@TempDir
 Path tempDownloadDir)
                   throws IOException,
NoSingleCellDataFoundException

This GEO series includes cell types in the barcodes.tsv.gz files.

Uses a chopped MEX fixture from the classpath; the over-the-wire variant is testGSE125708OverTheWire().

Throws:

IOException

NoSingleCellDataFoundException

testGSE125708OverTheWire

@Test
@Tag("slow") @Tag("network") @Tag("integration") @Tag("geo")
@NetworkAvailable(url="ftp://ftp.ncbi.nlm.nih.gov/geo/series/")
public void testGSE125708OverTheWire()
                              throws IOException,
NoSingleCellDataFoundException

Truth-source variant of testGSE125708(Path). Downloads the full GSE125708 bundle from NCBI FTP at test time and asserts against the upstream cell count. Kept as a regression guard so that the chopped fixture's faithfulness can be re-verified on demand.

Throws:

IOException

NoSingleCellDataFoundException