Uses of Annotation Interface
ubic.gemma.core.util.test.NetworkAvailable

Packages that use NetworkAvailable

Package	Description
ubic.gemma.apps
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.datastructure.matrix.io
ubic.gemma.core.loader.entrez
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.cellxgene
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.fetcher2
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.geo.singleCell
ubic.gemma.core.loader.expression.singleCell
ubic.gemma.core.loader.expression.singleCell.transform
ubic.gemma.core.loader.expression.sra
ubic.gemma.core.loader.expression.ucsc.cellbrowser
ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.ontology.ols
ubic.gemma.core.ontology.providers
ubic.gemma.core.util
ubic.gemma.persistence.service.expression.bioAssayData

Uses of NetworkAvailable in ubic.gemma.apps

Methods in ubic.gemma.apps with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	NCBIGene2GOAssociationLoaderCLITest.test()
final void	PubMedSearcherIntegrationTest.testMain()	Test method for AbstractCLI.executeCommand(CLIContext).

Uses of NetworkAvailable in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	ContinuousVariableDiffExTest.test()
void	DiffExWithInvalidInteractionTest.test()	This should automatically drop the interaction.
void	LowVarianceDataTest.test()
void	DiffExTest.testCountData()	Test differential expression analysis on RNA-seq data.
void	BaselineDetectionTest.testFetchAndLoadGSE18162()
void	DiffExTest.testGSE35930()	Test where probes have constant values.

Uses of NetworkAvailable in ubic.gemma.core.analysis.preprocess

Methods in ubic.gemma.core.analysis.preprocess with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	ProcessedExpressionDataCreateServiceTest.testComputeDevRankForExpressionExperimentMultiArrayWithGaps()	Three platforms, one sample was not run on GPL81.
void	TwoChannelExpressionDataDoubleMatrixTest.testMatrixConversion()
final void	MeanVarianceServiceTest.testServiceCreateCountData()
final void	MeanVarianceServiceTest.testServiceCreateExistingEe()
final void	MeanVarianceServiceTest.testServiceCreateOneColor()
final void	MeanVarianceServiceTest.testServiceCreateTwoColor()
void	SplitExperimentTest.testSplitGSE123753ByCollectionOfMaterial()
void	SplitExperimentTest.testSplitGSE17183ByOrganismPart()

Uses of NetworkAvailable in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	ExpressionExperimentBatchCorrectionServiceTest.testComBatOnEE()
void	RNASeqBatchInfoPopulationTest.testGetBatches()	Test of creating batch factor.
void	RNASeqBatchInfoPopulationTest.testGSE14285OneBatch()
void	RNASeqBatchInfoPopulationTest.testGSE156689NoBatchinfo()
void	BatchInfoPopulationServiceIntegrationTest.testLoad()
void	BatchInfoPopulationServiceIntegrationTest.testLoadCommandConsoleFormat()

Uses of NetworkAvailable in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	SVDServiceImplTest.testSvd()
void	SVDServiceImplTest.testSvdGapped()

Uses of NetworkAvailable in ubic.gemma.core.datastructure.matrix.io

Methods in ubic.gemma.core.datastructure.matrix.io with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	ExperimentalDesignWriterTest.testGSE1611()

Uses of NetworkAvailable in ubic.gemma.core.loader.entrez

Methods in ubic.gemma.core.loader.entrez with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	EutilFetchTest.testFetch()

Uses of NetworkAvailable in ubic.gemma.core.loader.entrez.pubmed

Classes in ubic.gemma.core.loader.entrez.pubmed with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	ExpressionExperimentBibRefFinderNetworkTest	The over-the-wire half of ExpressionExperimentBibRefFinderTest, which stubs GeoBrowser and never leaves the JVM.
class	PubMedSearchTest
class	PubMedXMLParserTest

Methods in ubic.gemma.core.loader.entrez.pubmed with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	PubMedXMLParserTest.testParseMulti()
void	PubMedXMLParserTest.testParseRetracted()
final void	PubMedXMLFetcherTest.testRetrieveByHTTP()
final void	PubMedXMLFetcherTest.testRetrieveByHTTP2()
final void	PubMedXMLFetcherTest.testRetrieveByHTTPBookshelf()
final void	PubMedXMLFetcherTest.testRetrieveByHTTPNotFound()

Uses of NetworkAvailable in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	DataUpdaterTest.testAddData()
void	ExpressionExperimentPlatformSwitchTest.testGSE36025()	for bug 3451
void	DataUpdaterTest.testLoadRNASeqData()
void	DataUpdaterTest.testLoadRNASeqDataWithMissingSamples()

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign with annotations of type NetworkAvailable

Modifier and Type	Method	Description
final void	ArrayDesignSequenceAlignmentandMappingTest.testProcessArrayDesign()
void	ArrayDesignSequenceProcessorFastacmdTest.testProcessArrayDesignWithFastaCmdFetch()

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.cellxgene

Classes in ubic.gemma.core.loader.expression.cellxgene with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	CellXGeneConverterTest
class	CellXGeneDataLoaderServiceTest
class	CellXGeneFetcherTest

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.geo

Classes in ubic.gemma.core.loader.expression.geo with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	GeoConverterTest2
class	GeoSingleCellDetectorTest	TODO: Phase 2 — trim and cache per-test download data so the integration-tagged methods can move to fully offline @Test.
class	GeoTermReplacementTest	Test replacements for GEO terms.

Methods in ubic.gemma.core.loader.expression.geo with annotations of type NetworkAvailable

Modifier and Type	Method	Description
final void	GeoConverterTest.test5C()
void	GeoSingleCellDetectorTest.testDownloadSingleCellDataInCellXGene()
void	GeoSingleCellDetectorTest.testDownloadSingleCellDataInCellXGeneWithoutACollectionId()
void	DatasetCombinerTest.testFindGDSGrouping()
void	DatasetCombinerTest.testFindGSE267()
void	DatasetCombinerTest.testFindGSEForGDS()
void	GeoSingleCellDetectorTest.testGSE125708()	This series has samples lacking data.
void	GeoSingleCellDetectorTest.testGSE147495()	This is a case of a MEX dataset where files are located in the series.
void	GeoSingleCellDetectorTest.testGSE155695()	This dataset has technical replicates, this is not supported.
void	GeoSingleCellDetectorTest.testGSE165635()	The SRA metadata does not use the "TRANSCRIPTOMIC SINGLE CELL" library source, but keywords in the protocol indicate it is single-cell.
void	GeoSingleCellDetectorTest.testGSE174574()	Interesting case because it uses genes.tsv instead of features.tsv.
void	GeoSingleCellDetectorTest.testGSE179516()	This is a Loom dataset with files in individual samples
void	GeoSingleCellDetectorTest.testGSE184506()	This series has complete MEX files at the sample-level, but also provide MEX files in the series.
void	GeoSingleCellDetectorTest.testGSE199762()	This one uses non-standard file names.
void	GeoSingleCellDetectorTest.testGSE202051()	This dataset has multiple .h5ad supplementary files.
void	GeoSingleCellDetectorTest.testGSE208742()	This dataset has MEX data at both series and sample-levels.
void	GeoSingleCellDetectorTest.testGSE218621()	This is a MEX dataset with a barcode_metadata.tsv.gz file.
void	GeoSingleCellDetectorTest.testGSE221522()
void	GeoSingleCellDetectorTest.testGSE242423()	This is a case of a MEX dataset that has matrix and barcodes at the sample-level (as we support it!), but genes at the series level.
void	GeoSingleCellDetectorTest.testGSE274772()
void	GeoSingleCellDetectorTest.testGSE71585()
void	GeoSingleCellDetectorTest.testHasSingleCellDataInCellXGene()
void	GeoSingleCellDetectorTest.testHasSingleCellDataInSra()

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.geo.fetcher2

Classes in ubic.gemma.core.loader.expression.geo.fetcher2 with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	GeoFetcherTest

Methods in ubic.gemma.core.loader.expression.geo.fetcher2 with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	GeoFetcherTest.testGSE246121ViaGeoQuery()	This is a fallback if we encounter issues with the FTP server.

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.geo.service

Classes in ubic.gemma.core.loader.expression.geo.service with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	GeoBrowserTest
class	GeoDatasetServiceTest	Test full procedure of loading GEO data, focus on corner cases.

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.geo.singleCell

Classes in ubic.gemma.core.loader.expression.geo.singleCell with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	GeoMexSingleCellDataLoaderConfigurerTest

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	MexSingleCellDataLoaderTest.testGSE125708OverTheWire()	Truth-source variant of MexSingleCellDataLoaderTest.testGSE125708(Path).
void	MexSingleCellDataLoaderTest.testGSE141552OverTheWire()	Truth-source variant of MexSingleCellDataLoaderTest.testGSE141552(Path).

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.singleCell.transform

Methods in ubic.gemma.core.loader.expression.singleCell.transform with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	SingleCell10xMexFilterTest.testGSM3559978()
void	SingleCell10xMexFilterTest.testGSM4871780()	This example uses 3 GEMs.
void	SingleCell10xMexFilterTest.testGSM8316309()

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.sra

Classes in ubic.gemma.core.loader.expression.sra with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	SraFetcherTest

Methods in ubic.gemma.core.loader.expression.sra with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	SraFetcherTest.testFetch()
void	SraFetcherTest.testFetchRunInfo()

Uses of NetworkAvailable in ubic.gemma.core.loader.expression.ucsc.cellbrowser

Methods in ubic.gemma.core.loader.expression.ucsc.cellbrowser with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	UcscCellBrowserUtilsTest.testGetDataset()
void	UcscCellBrowserUtilsTest.testGetDatasetDataMatrix()
void	UcscCellBrowserUtilsTest.testGetDatasetDescription()
void	UcscCellBrowserUtilsTest.testGetDatasets()

Uses of NetworkAvailable in ubic.gemma.core.loader.genome.gene.ncbi.homology

Methods in ubic.gemma.core.loader.genome.gene.ncbi.homology with annotations of type NetworkAvailable

Modifier and Type	Method	Description
final void	HomologeneServiceTest.testHomologeneFromFtpServer()

Uses of NetworkAvailable in ubic.gemma.core.ontology.ols

Methods in ubic.gemma.core.ontology.ols with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	OlsTermResolverIntegrationTest.testResolveFabricatedTermReturnsNull()
void	OlsTermResolverIntegrationTest.testResolveRealTerm()

Uses of NetworkAvailable in ubic.gemma.core.ontology.providers

Methods in ubic.gemma.core.ontology.providers with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	GemmaOntologyServiceTest.test()

Uses of NetworkAvailable in ubic.gemma.core.util

Classes in ubic.gemma.core.util with annotations of type NetworkAvailable

Modifier and Type	Class	Description
class	GemmaRestApiClientTest

Uses of NetworkAvailable in ubic.gemma.persistence.service.expression.bioAssayData

Methods in ubic.gemma.persistence.service.expression.bioAssayData with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	RawAndProcessedExpressionDataVectorServiceGeoTest.testFindByQt()
void	ProcessedExpressionDataVectorServiceTest.testGetProcessedDataMatrices()	Test method for ProcessedExpressionDataVectorService.getProcessedDataArrays(java.util.Collection, java.util.Collection) .