Package ubic.gemma.core.util

Interface CLI

All Known Implementing Classes:

AbstractAuthenticatedCLI, AbstractCLI, AffyDataFromCelCli, AffyProbeCollapseCli, ArrayDesignAlternativePopulateCli, ArrayDesignAnnotationFileCli, ArrayDesignAuditTrailCleanupCli, ArrayDesignBioSequenceDetachCli, ArrayDesignBlatCli, ArrayDesignMapSummaryCli, ArrayDesignMergeCli, ArrayDesignProbeCleanupCLI, ArrayDesignProbeMapperCli, ArrayDesignProbeRenamerCli, ArrayDesignRepeatScanCli, ArrayDesignSequenceAssociationCli, ArrayDesignSequenceManipulatingCli, ArrayDesignSubsumptionTesterCli, BatchEffectPopulationCli, BibRefUpdaterCli, BioSequenceCleanupCli, BlacklistCli, CtdDatabaseImporterCli, DatabaseViewGeneratorCLI, DeleteDiffExCli, DeleteEvidenceCLI, DeleteExperimentsCli, DgaDatabaseImporterCli, DifferentialExpressionAnalysisCli, EvidenceImporterAbstractCLI, EvidenceImporterCLI, ExperimentalDesignImportCli, ExperimentalDesignViewCli, ExperimentalDesignWriterCLI, ExpressionDataCorrMatCli, ExpressionDataMatrixWriterCLI, ExpressionExperimentDataFileGeneratorCli, ExpressionExperimentManipulatingCLI, ExpressionExperimentPlatformSwitchCli, ExpressionExperimentPrimaryPubCli, ExternalDatabaseAdderCli, ExternalDatabaseEvidenceImporterAbstractCLI, ExternalDatabaseOverviewCli, ExternalDatabaseUpdaterCli, ExternalFileGeneLoaderCLI, FactorValueMigratorCLI, FindObsoleteTermsCli, GeeqCli, GenericGenelistDesignGenerator, GeoGrabberCli, GwasDatabaseImporterCli, IndexGemmaCLI, LinkAnalysisCli, LoadEvidenceForClassifier, LoadExpressionDataCli, LoadSimpleExpressionDataCli, MakeExperimentPrivateCli, MakeExperimentsPublicCli, MeshTermFetcherCli, MultifunctionalityCli, NCBIGene2GOAssociationLoaderCLI, NcbiGeneLoaderCLI, OmimDatabaseImporterCli, OrderVectorsByDesignCli, ProcessedDataComputeCLI, PubMedLoaderCli, PubMedSearcher, ReplaceDataCli, RgdDatabaseImporterCli, RNASeqBatchInfoCli, RNASeqDataAddCli, SfariDatabaseImporterCli, SplitExperimentCli, SVDCli, TaxonLoaderCli, UpdateEE2CCli, UpdatePubMedCli, VectorMergingCli

public interface CLI

Interface for CLI tools.

Implementing this interface will make the tool detectable by GemmaCLI.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
boolean	allowPositionalArguments()	Indicate if this CLI allows positional arguments.
int	executeCommand(String... args)	Execute the given command given CLI arguments.
GemmaCLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
String	getCommandName()	A short memorable name for the command that can be used to locate this class.
org.apache.commons.cli.Options	getOptions()	Obtain the options for the CLI.
String	getShortDesc()	Obtain a short description for this command explaining what it does.

Method Detail

getCommandName

@Nullable
String getCommandName()

A short memorable name for the command that can be used to locate this class.

Returns:

name; if null or blank, this will not be available as a shortcut command.

getShortDesc

@Nullable
String getShortDesc()

Obtain a short description for this command explaining what it does.

getCommandGroup

GemmaCLI.CommandGroup getCommandGroup()

Obtain the command group for this CLI.

getOptions

org.apache.commons.cli.Options getOptions()

Obtain the options for the CLI.

allowPositionalArguments

boolean allowPositionalArguments()

Indicate if this CLI allows positional arguments.

executeCommand

int executeCommand(String... args)

Execute the given command given CLI arguments.

Returns:

an exit code