Uses of Interface
ubic.gemma.cli.util.CLI

Packages that use CLI

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.cli.util

Uses of CLI in ubic.gemma.apps

Classes in ubic.gemma.apps that implement CLI

Modifier and Type	Class	Description
class	AffyDataFromCelCli	Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
class	AffyProbeCollapseCli	Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
class	ArrayDesignAlternativePopulateCli	This only needs to be re-run when the mappings change.
class	ArrayDesignAnnotationFileCli	Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
class	ArrayDesignAuditTrailCleanupCli	work in progress
class	ArrayDesignBioSequenceDetachCli	Remove all associations that this array design has with BioSequences.
class	ArrayDesignBlatCli	Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
class	ArrayDesignMapSummaryCli	CLI for ArrayDesignMapSummaryService
class	ArrayDesignMergeCli	make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
class	ArrayDesignProbeCleanupCLI	Delete design elements (probes) that are invalid for one reason or another.
class	ArrayDesignProbeMapperCli	Process the blat results for an array design to map them onto genes.
class	ArrayDesignProbeRenamerCli	Deprecated. renaming probes is not a good idea in general
class	ArrayDesignRepeatScanCli	Runs repeatmasker on array designs.
class	ArrayDesignSequenceAssociationCli	Attach sequences to array design, fetching from BLAST database if requested.
class	ArrayDesignSequenceManipulatingCli	Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
class	ArrayDesignSubsumptionTesterCli	Test two array designs to see if one subsumes the other, and if so update their information.
class	BatchEffectPopulationCli	For bulk processing of batch-info-fetching.
class	BibRefUpdaterCli	Refreshes the information in all the bibliographic references in the system.
class	BioSequenceCleanupCli	Goes through the biosequences for array designs in the database and removes duplicates.
class	BlacklistCli	Add entries to the blacklist
class	CellLevelMetadataWriterCli
class	CompleteCli	This CLI provide various runtime completions that can be re-used by other CLIs.
class	DatabaseViewGeneratorCLI	Simple driver of DatabaseViewGenerator.
class	DeleteDiffExCli	Delete differential expression analsyes on a per-experiment basis.
class	DeleteExperimentsCli	Delete one or more experiments from the system.
class	DetectQuantitationTypeCli
class	DifferentialExpressionAnalysisCli	A command line interface to the DifferentialExpressionAnalysis.
class	DifferentialExpressionAnalysisWriterCli	Writes differential expression analysis files to disk.
class	ExperimentalDesignImportCli
class	ExperimentalDesignViewCli
class	ExperimentalDesignWriterCLI	Writes out the experimental design for a given experiment.
class	ExpressionDataCorrMatCli	Create correlation visualizations for expression experiments
class	ExpressionDataMatrixWriterCLI	Prints preferred data matrix to a file.
class	ExpressionExperimentDataFileGeneratorCli	Deprecated. use DifferentialExpressionAnalysisWriterCli instead.
class	ExpressionExperimentDataUpdaterCli	Update GEO data for an experiment.
class	ExpressionExperimentManipulatingCLI	Base class for CLIs that needs one or more expression experiment as an input.
class	ExpressionExperimentMetadataChangelogEntryAdderCli	CLI tool for adding manual entries to the changelog file of an experiment.
class	ExpressionExperimentMetadataChangelogViewerCli	CLI tool for viewing the changelog file of an experiment.
class	ExpressionExperimentMetadataFileAdderCli	Add a metadata file to an experiment and record an entry in the changelog file.
class	ExpressionExperimentPlatformSwitchCli	Switch the array design used to the merged one.
class	ExpressionExperimentPrimaryPubCli	Update the primary publication for experiments.
class	ExpressionExperimentVectorsManipulatingCli<T extends DataVector>	Base class for CLI tools that manipulate expression experiment vectors.
class	ExternalDatabaseAdderCli	Add a new external database, but requires editing the code to do so.
class	ExternalDatabaseOverviewCli
class	ExternalDatabaseUpdaterCli
class	ExternalFileGeneLoaderCLI	CLI for loading genes from a non NCBI files.
class	FactorValueMigratorCLI	Deprecated. this will be removed as soon as all the old-style characteristics are migrated
class	FindObsoleteTermsCli
class	FixOntologyTermLabelsCli
class	GeeqCli	Generate or update GEEQ scores
class	GenerateDatabaseUpdateCli	Generate a database update script.
class	GenericGenelistDesignGenerator	Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.
class	GeoGrabberCli	Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening.
class	IndexGemmaCLI
class	InitializeDatabaseCli	Initialize the database.
class	LinkAnalysisCli	Commandline tool to conduct link (coexpression) analysis.
class	ListExpressionDataFIleLocksCli	List all locks within Gemma's data directories.
class	ListQuantitationTypesCli
class	LoadExpressionDataCli	Simple command line to load expression experiments, either singly or in batches defined on the command line or in a file.
class	LoadSimpleExpressionDataCli	Command Line tools for loading the expression experiment in flat files
class	LockExpressionDataFileCli	This CLI allows one to lock an experiment data or metadata file.
class	MakeExperimentPrivateCli
class	MakeExperimentsPublicCli	Make data sets public.
class	MeshTermFetcherCli	Deprecated. should not be part of Gemma main code
class	MultifunctionalityCli
class	NCBIGene2GOAssociationLoaderCLI	Load GO -> gene associations from NCBI.
class	NcbiGeneLoaderCLI	Command line interface to gene parsing and loading
class	OrderVectorsByDesignCli	Use to change the order of the values to match the experimental design.
class	ProcessedDataComputeCLI	Prepare the "processed" expression data vectors, and can also do batch correction.
class	ProcessedDataDeleterCli
class	ProtocolAdderCli
class	ProtocolDeleterCli
class	ProtocolListCli
class	PubMedLoaderCli	Load PubMed files from XML files -- not used routinely!
class	PubMedSearcher	Simple application to perform pubmed searches from a list of terms, and persist the results in the database.
class	RawDataDeleterCli
class	RawExpressionDataWriterCli
class	RefreshExperimentCli
class	ReplaceDataCli	Replace data in an existing data set.
class	RNASeqBatchInfoCli	Deprecated. this should not be necessary and the regular batch population tool can be used instead.
class	RNASeqDataAddCli	Designed to add count and/or RPKM data to a data set that has only meta-data.
class	SingleCellDataAggregateDeleterCli
class	SingleCellDataAggregatorCli
class	SingleCellDataDeleterCli
class	SingleCellDataDownloaderCli
class	SingleCellDataLoaderCli
class	SingleCellDataTransformCli	Transform various single-cell formats.
class	SingleCellDataWriterCli
class	SingleCellSparsityMetricsUpdaterCli
class	SplitExperimentCli	Split an experiment into parts based on an experimental factor
class	SVDCli
class	TaxonLoaderCli
class	UnifiedOntologyUpdaterCli
class	UpdateDatabaseCli	Update the database.
class	UpdateEe2AdCli
class	UpdateEE2CCli
class	UpdateGene2CsCli
class	UpdatePubMedCli	Identify experiments in Gemma that have no publication Fetch their GEO records and check for pubmed IDs Add the publications where we find them.
class	VectorMergingCli	For experiments that used multiple array designs, merge the expression profiles

Uses of CLI in ubic.gemma.cli.util

Classes in ubic.gemma.cli.util that implement CLI

Modifier and Type	Class	Description
class	AbstractAuthenticatedCLI	Subclass this to create command line interface (CLI) tools that need authentication.
class	AbstractAutoSeekingCLI<T extends Auditable>	Provide auto-seeking capabilities to a CLI.
class	AbstractCLI	Basic implementation of the CLI interface.