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

Class MexSingleCellDataLoaderTest

java.lang.Object

org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

ubic.gemma.core.util.test.BaseTest

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

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

@ContextConfiguration
public class MexSingleCellDataLoaderTest
extends BaseTest

Field Summary

Fields

Modifier and Type	Field	Description
final NetworkAvailableRule	networkAvailableRule

Fields inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

applicationContext, logger

Constructor Summary

Constructors

Constructor	Description
MexSingleCellDataLoaderTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	testEmpty()
void	testGSE125708()	This GEO series inclues cell types in the barcodes.tsv.gz files.
void	testGSE141552()	This dataset does not filter empty droplets and thus many barcodes are simply unused and can be discarded.
void	testGSE224438()
void	testLoadSpecificSamples()
void	testUnmatchedSample()

Methods inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

setApplicationContext

Methods inherited from class java.lang.Object

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

Field Details

networkAvailableRule

public final NetworkAvailableRule networkAvailableRule

Constructor Details

MexSingleCellDataLoaderTest

public MexSingleCellDataLoaderTest()

Method Details

setUp

public void setUp()
           throws IOException

Throws:

IOException

testEmpty

public void testEmpty()
               throws IOException

Throws:

IOException

testGSE224438

public void testGSE224438()
                   throws IOException

Throws:

IOException

testLoadSpecificSamples

public void testLoadSpecificSamples()
                             throws IOException

Throws:

IOException

testUnmatchedSample

public void testUnmatchedSample()
                         throws IOException

Throws:

IOException

testGSE141552

@NetworkAvailable(url="ftp://ftp.ncbi.nlm.nih.gov/geo/series/")
public void testGSE141552()
                   throws IOException,
NoSingleCellDataFoundException

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

Throws:

IOException

NoSingleCellDataFoundException

testGSE125708

@NetworkAvailable(url="ftp://ftp.ncbi.nlm.nih.gov/geo/series/")
public void testGSE125708()
                   throws IOException,
NoSingleCellDataFoundException

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

Throws:

IOException

NoSingleCellDataFoundException