Uses of Annotation Type
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.arrayExpress
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.providers
ubic.gemma.core.search
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	PubMedSearchTest
class	PubMedXMLParserTest

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

Modifier and Type	Method	Description
void	ExpressionExperimentBibRefFinderTest.testLocatePrimaryReference()
void	ExpressionExperimentBibRefFinderTest.testLocatePrimaryReferenceInvalidGSE()
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.arrayExpress

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

Modifier and Type	Method	Description
final void	SDRFFetcherTest.testFetch()

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

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

Modifier and Type	Method	Description
void	CellXGeneAnnDataSingleCellDataLoaderTest.testKeepPooledSample()

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: move SOFT files in test resources and mock FTP downloads
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	DatasetCombinerTest.testFindGDSGrouping()
void	DatasetCombinerTest.testFindGSE267()
void	DatasetCombinerTest.testFindGSEForGDS()

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.

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

Modifier and Type	Method	Description
final void	GeoBrowserServiceTest.testFillDetails()
void	GeoBrowserTest.testGetRecentGeoRecords()
final void	GeoBrowserServiceTest.testGetRecentRecords()
void	GeoBrowserServiceParseTest.testParse()
void	GeoBrowserServiceParseTest.testParse2()
void	GeoBrowserServiceParseTest.testParse3()

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.testGSE125708()	This GEO series inclues cell types in the barcodes.tsv.gz files.
void	MexSingleCellDataLoaderTest.testGSE141552()	This dataset does not filter empty droplets and thus many barcodes are simply unused and can be discarded.

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.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.search

Methods in ubic.gemma.core.search with annotations of type NetworkAvailable

Modifier and Type	Method	Description
void	SearchServiceIntegrationTest.testSearchByBibRefIdProblems()
void	SearchServiceIntegrationTest.testSearchByBibRefIdProblemsB()

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) .