Package ubic.gemma.cli.util

Interface CLI

All Known Implementing Classes:
AbstractAuthenticatedCLI, AbstractAutoSeekingCLI, AbstractCLI, AffyDataFromCelCli, AffyProbeCollapseCli, ArrayDesignAlternativePopulateCli, ArrayDesignAnnotationFileCli, ArrayDesignAuditTrailCleanupCli, ArrayDesignBioSequenceDetachCli, ArrayDesignBlatCli, ArrayDesignMapSummaryCli, ArrayDesignMergeCli, ArrayDesignProbeCleanupCLI, ArrayDesignProbeMapperCli, ArrayDesignProbeRenamerCli, ArrayDesignRepeatScanCli, ArrayDesignSequenceAssociationCli, ArrayDesignSequenceManipulatingCli, ArrayDesignSubsumptionTesterCli, BatchEffectPopulationCli, BibRefUpdaterCli, BioSequenceCleanupCli, BlacklistCli, CellLevelMetadataWriterCli, CompleteCli, DatabaseViewGeneratorCLI, DeleteDiffExCli, DeleteExperimentsCli, DetectQuantitationTypeCli, DifferentialExpressionAnalysisCli, DifferentialExpressionAnalysisWriterCli, ExperimentalDesignImportCli, ExperimentalDesignViewCli, ExperimentalDesignWriterCLI, ExpressionDataCorrMatCli, ExpressionDataMatrixWriterCLI, ExpressionExperimentDataFileGeneratorCli, ExpressionExperimentDataUpdaterCli, ExpressionExperimentManipulatingCLI, ExpressionExperimentMetadataChangelogEntryAdderCli, ExpressionExperimentMetadataChangelogViewerCli, ExpressionExperimentMetadataFileAdderCli, ExpressionExperimentPlatformSwitchCli, ExpressionExperimentPrimaryPubCli, ExpressionExperimentVectorsManipulatingCli, ExternalDatabaseAdderCli, ExternalDatabaseOverviewCli, ExternalDatabaseUpdaterCli, ExternalFileGeneLoaderCLI, FactorValueMigratorCLI, FindObsoleteTermsCli, FixOntologyTermLabelsCli, GeeqCli, GenerateDatabaseUpdateCli, GenericGenelistDesignGenerator, GeoGrabberCli, IndexGemmaCLI, InitializeDatabaseCli, LinkAnalysisCli, ListExpressionDataFIleLocksCli, ListQuantitationTypesCli, LoadExpressionDataCli, LoadSimpleExpressionDataCli, LockExpressionDataFileCli, MakeExperimentPrivateCli, MakeExperimentsPublicCli, MeshTermFetcherCli, MultifunctionalityCli, NCBIGene2GOAssociationLoaderCLI, NcbiGeneLoaderCLI, OrderVectorsByDesignCli, ProcessedDataComputeCLI, ProcessedDataDeleterCli, ProtocolAdderCli, ProtocolDeleterCli, ProtocolListCli, PubMedLoaderCli, PubMedSearcher, RawDataDeleterCli, RawExpressionDataWriterCli, RefreshExperimentCli, ReplaceDataCli, RNASeqBatchInfoCli, RNASeqDataAddCli, SingleCellDataAggregateDeleterCli, SingleCellDataAggregatorCli, SingleCellDataDeleterCli, SingleCellDataDownloaderCli, SingleCellDataLoaderCli, SingleCellDataTransformCli, SingleCellDataWriterCli, SingleCellSparsityMetricsUpdaterCli, SplitExperimentCli, SVDCli, TaxonLoaderCli, UnifiedOntologyUpdaterCli, UpdateDatabaseCli, UpdateEe2AdCli, UpdateEE2CCli, UpdateGene2CsCli, UpdatePubMedCli, VectorMergingCli
public interface CLI
Interface for CLI tools.

Implementing this interface will make the tool detectable by

invalid reference 
GemmaCLI
.
Author:
poirigui

  • Method Details

    • 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.

    • getCommandAliases

      List<String> getCommandAliases()
      A list of aliases for the command that can be used to locate this class.

    • getShortDesc

      @Nullable String getShortDesc()
      Obtain a short description for this command explaining what it does.

    • getCommandGroup

      CLI.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

      void executeCommand(CLIContext ctx)
      Execute the given command given CLI arguments.