A B C E F G L M N O P R S T U W
All Classes All Packages

A

allowPositionalArguments() - Method in class ubic.gemma.apps.TestCli

arrayDesignMergeCli() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

ArrayDesignMergeCliTest - Class in ubic.gemma.apps

ArrayDesignMergeCliTest() - Constructor for class ubic.gemma.apps.ArrayDesignMergeCliTest

ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration - Class in ubic.gemma.apps

ArrayDesignMergeCliTestContextConfiguration() - Constructor for class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

arrayDesignMergeService() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

arrayDesignReportService() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

arrayDesignService() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

Assertions - Class in ubic.gemma.cli.util.test

Assertions() - Constructor for class ubic.gemma.cli.util.test.Assertions

assertThat(CLI) - Static method in class ubic.gemma.cli.util.test.Assertions

auditEventService() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

auditTrailService() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

AuthenticatedCliTestConfig - Class in ubic.gemma.cli.util.test

A base class with mocks for testing CLI commands that require authentication.

AuthenticatedCliTestConfig() - Constructor for class ubic.gemma.cli.util.test.AuthenticatedCliTestConfig

B

BaseCliIntegrationTest - Class in ubic.gemma.cli.util.test

Base class for CLI integration tests.

BaseCliIntegrationTest() - Constructor for class ubic.gemma.cli.util.test.BaseCliIntegrationTest

BaseCliTest - Class in ubic.gemma.cli.util.test

Base class for CLI tests.

BaseCliTest() - Constructor for class ubic.gemma.cli.util.test.BaseCliTest

BatchProcessingCliTest - Class in ubic.gemma.apps

BatchProcessingCliTest() - Constructor for class ubic.gemma.apps.BatchProcessingCliTest

C

CliAssert - Class in ubic.gemma.cli.util.test

CliAssert(CLI) - Constructor for class ubic.gemma.cli.util.test.CliAssert

cliAuthenticationManager() - Method in class ubic.gemma.cli.util.test.AuthenticatedCliTestConfig

CompletionGeneratorTest - Class in ubic.gemma.cli.util

CompletionGeneratorTest() - Constructor for class ubic.gemma.cli.util.CompletionGeneratorTest

E

entityLocator() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

EnumConverterTest - Class in ubic.gemma.cli.util

EnumConverterTest() - Constructor for class ubic.gemma.cli.util.EnumConverterTest

executeCommand(CliContext) - Method in class ubic.gemma.apps.TestCli

ExternalDatabaseUpdaterCliTest - Class in ubic.gemma.apps

ExternalDatabaseUpdaterCliTest() - Constructor for class ubic.gemma.apps.ExternalDatabaseUpdaterCliTest

F

FactorValueMigratorCLITest - Class in ubic.gemma.apps

Deprecated.

FactorValueMigratorCLITest() - Constructor for class ubic.gemma.apps.FactorValueMigratorCLITest

Deprecated.

FactorValueMigratorServiceTest - Class in ubic.gemma.apps

Deprecated.

FactorValueMigratorServiceTest() - Constructor for class ubic.gemma.apps.FactorValueMigratorServiceTest

Deprecated.

fails() - Method in class ubic.gemma.cli.util.test.CliAssert

failsWith(int) - Method in class ubic.gemma.cli.util.test.CliAssert

FindObsoleteTermsCliTest - Class in ubic.gemma.apps

FindObsoleteTermsCliTest() - Constructor for class ubic.gemma.apps.FindObsoleteTermsCliTest

G

GemmaCLITest - Class in ubic.gemma.cli.main

GemmaCLITest() - Constructor for class ubic.gemma.cli.main.GemmaCLITest

gemmaRestApiClient() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

GeoGrabberCliTest - Class in ubic.gemma.apps

GeoGrabberCliTest() - Constructor for class ubic.gemma.apps.GeoGrabberCliTest

getArguments() - Method in class ubic.gemma.cli.util.TestCliContext

getCommandAliases() - Method in class ubic.gemma.apps.TestCli

getCommandGroup() - Method in class ubic.gemma.apps.TestCli

getCommandName() - Method in class ubic.gemma.apps.TestCli

getCommandNameOrAliasUsed() - Method in class ubic.gemma.cli.util.TestCliContext

getConsole() - Method in class ubic.gemma.cli.util.TestCliContext

getEnvironment() - Method in class ubic.gemma.cli.util.TestCliContext

getErrorStream() - Method in class ubic.gemma.cli.util.TestCliContext

getInputStream() - Method in class ubic.gemma.cli.util.TestCliContext

getOptions() - Method in class ubic.gemma.apps.TestCli

getOutputStream() - Method in class ubic.gemma.cli.util.TestCliContext

getShortDesc() - Method in class ubic.gemma.apps.TestCli

L

LoadSimpleExpressionDataCliTest - Class in ubic.gemma.apps

LoadSimpleExpressionDataCliTest() - Constructor for class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

M

manualAuthenticationService() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest.ArrayDesignMergeCliTestContextConfiguration

MarkCLIsAsPrototypesTest - Class in ubic.gemma.cli.util

Test various behaviours of CLIs when injected as bean.

MarkCLIsAsPrototypesTest() - Constructor for class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

MeterRegistryCliConfigurerTest - Class in ubic.gemma.cli.metrics

MeterRegistryCliConfigurerTest() - Constructor for class ubic.gemma.cli.metrics.MeterRegistryCliConfigurerTest

N

NCBIGene2GOAssociationLoaderCLITest - Class in ubic.gemma.apps

NCBIGene2GOAssociationLoaderCLITest() - Constructor for class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLITest

O

OptionsUtilsTest - Class in ubic.gemma.cli.util

OptionsUtilsTest() - Constructor for class ubic.gemma.cli.util.OptionsUtilsTest

P

ProtocolAdderCliTest - Class in ubic.gemma.apps

ProtocolAdderCliTest() - Constructor for class ubic.gemma.apps.ProtocolAdderCliTest

ProtocolDeleterCliTest - Class in ubic.gemma.apps

ProtocolDeleterCliTest() - Constructor for class ubic.gemma.apps.ProtocolDeleterCliTest

PubMedSearcherIntegrationTest - Class in ubic.gemma.apps

Tests command line.

PubMedSearcherIntegrationTest() - Constructor for class ubic.gemma.apps.PubMedSearcherIntegrationTest

R

resetMocks() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

resetMocks() - Method in class ubic.gemma.apps.ProtocolAdderCliTest

resetTimeZone() - Static method in class ubic.gemma.cli.util.OptionsUtilsTest

RNASeqDataAddCliTest - Class in ubic.gemma.apps

RNASeqDataAddCliTest() - Constructor for class ubic.gemma.apps.RNASeqDataAddCliTest

S

setArguments(String[]) - Method in class ubic.gemma.cli.util.TestCliContext

setCommandNameOrAliasUsed(String) - Method in class ubic.gemma.cli.util.TestCliContext

setConsole(Console) - Method in class ubic.gemma.cli.util.TestCliContext

setEnvironment(Map<String, String>) - Method in class ubic.gemma.cli.util.TestCliContext

setErrorStream(PrintStream) - Method in class ubic.gemma.cli.util.TestCliContext

setInputStream(InputStream) - Method in class ubic.gemma.cli.util.TestCliContext

setOutputStream(PrintStream) - Method in class ubic.gemma.cli.util.TestCliContext

setTimeZoneToAmericaVancouver() - Static method in class ubic.gemma.cli.util.OptionsUtilsTest

setUp() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCliTest

setUp() - Method in class ubic.gemma.apps.FactorValueMigratorCLITest

Deprecated.

setUp() - Method in class ubic.gemma.apps.FactorValueMigratorServiceTest

Deprecated.

setUp() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

ShellUtilsTest - Class in ubic.gemma.cli.util

ShellUtilsTest() - Constructor for class ubic.gemma.cli.util.ShellUtilsTest

SingleCellDataDownloaderCliTest - Class in ubic.gemma.apps

SingleCellDataDownloaderCliTest() - Constructor for class ubic.gemma.apps.SingleCellDataDownloaderCliTest

standardError() - Method in class ubic.gemma.cli.util.test.CliAssert

standardOutput() - Method in class ubic.gemma.cli.util.test.CliAssert

succeeds() - Method in class ubic.gemma.cli.util.test.CliAssert

Asserts that the command succeeds with a zero exit status.

T

tearDown() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest

tearDown() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCliTest

tearDown() - Method in class ubic.gemma.apps.FactorValueMigratorServiceTest

Deprecated.

tearDown() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

test() - Method in class ubic.gemma.apps.ArrayDesignMergeCliTest

test() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCliTest

test() - Method in class ubic.gemma.apps.FindObsoleteTermsCliTest

test() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLITest

test() - Method in class ubic.gemma.apps.ProtocolAdderCliTest

test() - Method in class ubic.gemma.apps.ProtocolDeleterCliTest

test() - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurerTest

test() - Method in class ubic.gemma.cli.util.EnumConverterTest

test() - Method in class ubic.gemma.cli.util.ShellUtilsTest

testBash() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

testBashCompletions() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

TestCli - Class in ubic.gemma.apps

TestCli() - Constructor for class ubic.gemma.apps.TestCli

testCliBeanIsPrototype() - Method in class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

TestCliContext - Class in ubic.gemma.cli.util

A simple implementation of CliContext for testing purposes.

TestCliContext(String, String[]) - Constructor for class ubic.gemma.cli.util.TestCliContext

testDownloadSingleSampleAccession() - Method in class ubic.gemma.apps.SingleCellDataDownloaderCliTest

testExtractKeywords() - Method in class ubic.gemma.apps.GeoGrabberCliTest

testFish() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

testFishCompletions() - Method in class ubic.gemma.cli.util.CompletionGeneratorTest

testLoadMetadata() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

testLoadMetadataFileLackingHeader() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

Convers old-style files that lack a header.

testLoadMetadataWithoutData() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCliTest

testMain() - Method in class ubic.gemma.apps.PubMedSearcherIntegrationTest

Test method for AbstractCLI.executeCommand(CliContext).

testMaskPwd() - Method in class ubic.gemma.cli.main.GemmaCLITest

testMigrateFactorValues() - Method in class ubic.gemma.apps.FactorValueMigratorCLITest

Deprecated.

testMigrationThatReuseObject() - Method in class ubic.gemma.apps.FactorValueMigratorServiceTest

Deprecated.

testMigrationThatReusesExistingStatement() - Method in class ubic.gemma.apps.FactorValueMigratorServiceTest

Deprecated.

testMigrationWithFreeTextSubject() - Method in class ubic.gemma.apps.FactorValueMigratorServiceTest

Deprecated.

testPaired() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

testParallelAndSequentialCli() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testParallelCli() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testParseFuzzyDate() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

testParseIso8601Date() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

testParseWords() - Method in class ubic.gemma.cli.util.OptionsUtilsTest

testReporting() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testSequentialCli() - Method in class ubic.gemma.apps.BatchProcessingCliTest

testSingletonShouldNotBeInitializedEagerly() - Method in class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

testUnpaired() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

testUnrelatedBeanIsSingleton() - Method in class ubic.gemma.cli.util.MarkCLIsAsPrototypesTest

testWhenPairednessIsUnknown() - Method in class ubic.gemma.apps.RNASeqDataAddCliTest

testWhenProtocolWithNameAlreadyExists() - Method in class ubic.gemma.apps.ProtocolAdderCliTest

U

ubic.gemma.apps - package ubic.gemma.apps

ubic.gemma.cli.main - package ubic.gemma.cli.main

ubic.gemma.cli.metrics - package ubic.gemma.cli.metrics

ubic.gemma.cli.util - package ubic.gemma.cli.util

ubic.gemma.cli.util.test - package ubic.gemma.cli.util.test

W

withArguments(String...) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the arguments passed to the command.

withCommandNameOrAlias(String) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the command name or alias used to execute the command.

withConsole(Console) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the console to be used for interactive use.

withEnvironment(Map<String, String>) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the environment variables to be used when executing the command.

withErrorStream(OutputStream) - Method in class ubic.gemma.cli.util.test.CliAssert

withInputStream(InputStream) - Method in class ubic.gemma.cli.util.test.CliAssert

Set the input stream to be used as standard input for the command.

withOutputStream(OutputStream) - Method in class ubic.gemma.cli.util.test.CliAssert

A B C E F G L M N O P R S T U W
All Classes All Packages