All Classes Interface Summary Class Summary Enum Summary
| Class |
Description |
| AbstractAuthenticatedCLI |
Subclass this to create command line interface (CLI) tools that need authentication.
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| AbstractAutoSeekingCLI<T extends ubic.gemma.model.common.auditAndSecurity.Auditable> |
Provide auto-seeking capabilities to a CLI.
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| AbstractCLI |
Basic implementation of the CLI interface. |
| AbstractCompletionGenerator |
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| AbstractDelegatingExecutorService |
A delegating executor service inspired by DelegatingSecurityContextExecutorService.
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| AffyDataFromCelCli |
Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
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| AffyProbeCollapseCli |
Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
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| ArrayDesignAlternativePopulateCli |
This only needs to be re-run when the mappings change.
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| 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.
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| ArrayDesignAuditTrailCleanupCli |
work in progress
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| ArrayDesignBioSequenceDetachCli |
Remove all associations that this array design has with BioSequences.
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| ArrayDesignBlatCli |
Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
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| ArrayDesignMapSummaryCli |
CLI for ArrayDesignMapSummaryService
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| 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.
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| ArrayDesignProbeCleanupCLI |
Delete design elements (probes) that are invalid for one reason or another.
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| ArrayDesignProbeMapperCli |
Process the blat results for an array design to map them onto genes.
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| ArrayDesignProbeRenamerCli |
Deprecated.
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| ArrayDesignRepeatScanCli |
Runs repeatmasker on array designs.
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| ArrayDesignSequenceAssociationCli |
Attach sequences to array design, fetching from BLAST database if requested.
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| ArrayDesignSequenceManipulatingCli |
Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something
with it.
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| ArrayDesignSubsumptionTesterCli |
Test two array designs to see if one subsumes the other, and if so update their information.
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| BashCompletionGenerator |
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| BatchEffectPopulationCli |
For bulk processing of batch-info-fetching.
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| BatchTaskExecutorService |
A task executor that automatically reports errors in batch tasks.
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| BatchTaskProcessingResult |
Represents an individual result in a batch processing.
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| BatchTaskProgressReporter |
Report progress on batch tasks.
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| BatchTaskSummaryWriter |
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| BibRefUpdaterCli |
Refreshes the information in all the bibliographic references in the system.
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| BioSequenceCleanupCli |
Goes through the biosequences for array designs in the database and removes duplicates.
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| BlacklistCli |
Add entries to the blacklist
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| CLI |
Interface for CLI tools.
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| CLI.CommandGroup |
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| CLIAuthenticationAware |
Interface for a component that should receive the username/password authentication token from the CLI.
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| CLIAuthenticationManager |
Manages authentication from the CLI.
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| CliContext |
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| CompleteCli |
This CLI provide various runtime completions that can be re-used by other CLIs.
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| CompletionGenerator |
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| CompletionSource |
Defines a source of completions.
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| CompletionSource.Completion |
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| CompletionType |
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| CompletionUtils |
Utilities for generating completions.
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| CompositeBatchTaskSummaryWriter |
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| ConfigurationLinter |
Lint various aspects of the configuration for the CLI profile.
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| DatabaseViewGeneratorCLI |
Simple driver of DatabaseViewGenerator.
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| DeleteDiffExCli |
Delete differential expression analsyes on a per-experiment basis.
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| DeleteExperimentsCli |
Delete one or more experiments from the system.
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| DetectQuantitationTypeCli |
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| DifferentialExpressionAnalysisCli |
A command line interface to the DifferentialExpressionAnalysis.
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| EntityLocator |
Locate various entities using identifiers supplied by the CLI.
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| EntityLocatorImpl |
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| EntityOptionsUtils |
Utilities for adding options to the CLI that can subsequently be retrieved with EntityLocator. |
| EnumConverter<T extends Enum<T>> |
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| EnumeratedByCommandConverter<T,E extends Throwable> |
This interface is implemented by Converter that can use an external command to get possible values.
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| EnumeratedByCommandStringConverter |
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| EnumeratedConverter<T,E extends Throwable> |
This interface is implemented by converters that can enumerate their possible values.
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| EnumeratedStringConverter |
A string converter that can only convert from a finite set of possible values.
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| ExperimentalDesignImportCli |
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| ExperimentalDesignViewCli |
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| ExperimentalDesignWriterCLI |
Writes out the experimental design for a given experiment.
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| ExpressionDataCorrMatCli |
Create correlation visualizations for expression experiments
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| ExpressionDataMatrixWriterCLI |
Prints preferred data matrix to a file.
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| ExpressionExperimentDataFileGeneratorCli |
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| ExpressionExperimentDataUpdaterCli |
Update GEO data for an experiment.
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| ExpressionExperimentManipulatingCLI |
Base class for CLIs that needs one or more expression experiment as an input.
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| ExpressionExperimentMetadataChangelogEntryAdderCli |
CLI tool for adding manual entries to the changelog file of an experiment.
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| ExpressionExperimentMetadataChangelogViewerCli |
CLI tool for viewing the changelog file of an experiment.
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| ExpressionExperimentMetadataFileAdderCli |
Add a metadata file to an experiment and record an entry in the changelog file.
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| ExpressionExperimentPlatformSwitchCli |
Switch the array design used to the merged one.
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| ExpressionExperimentPrimaryPubCli |
Update the primary publication for experiments.
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| ExpressionExperimentVectorsManipulatingCli<T extends ubic.gemma.model.expression.bioAssayData.DataVector> |
Base class for CLI tools that manipulate expression experiment vectors.
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| ExternalDatabaseAdderCli |
Add a new external database, but requires editing the code to do so.
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| ExternalDatabaseOverviewCli |
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| ExternalDatabaseUpdaterCli |
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| ExternalFileGeneLoaderCLI |
CLI for loading genes from a non NCBI files.
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| FactorValueMigratorCLI |
Deprecated.
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| FileUtils |
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| FindObsoleteTermsCli |
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| FishCompletionGenerator |
Generates fish completion script.
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| FixOntologyTermLabelsCli |
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| GeeqCli |
Generate or update GEEQ scores
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| GemmaCLI |
Generic command line for Gemma.
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| GemmaRestApiClientAuthenticator |
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| GemmaRestApiClientConfig |
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| GenerateDatabaseUpdateCli |
Generate a database update script.
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| GenericGenelistDesignGenerator |
Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.
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| GeoGrabberCli |
Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further
screening.
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| HelpUtils |
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| IndexGemmaCLI |
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| InitializeDatabaseCli |
Initialize the database.
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| LinkAnalysisCli |
Commandline tool to conduct link (coexpression) analysis.
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| ListExpressionDataFIleLocksCli |
List all locks within Gemma's data directories.
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| ListQuantitationTypesCli |
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| LoadExpressionDataCli |
Simple command line to load expression experiments, either singly or in batches defined on the command line or in a
file.
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| LoadSimpleExpressionDataCli |
Command Line tools for loading the expression experiment in flat files
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| LockExpressionDataFileCli |
This CLI allows one to lock an experiment data or metadata file.
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| Log4jConfigurer |
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| LoggerCompletionSource |
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| LoggingBatchTaskSummaryWriter |
Task summary writer that logs the result of a batch task to a logger.
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| LoggingConfigurer |
Simple interface for configuring logging levels.
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| MakeExperimentPrivateCli |
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| MakeExperimentsPublicCli |
Make data sets public.
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| MeshTermFetcherCli |
Deprecated.
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| MeterRegistryCliConfigurer |
This configurer adds two tags: environment='cli' and user to the given meter registry.
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| MultifunctionalityCli |
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| NCBIGene2GOAssociationLoaderCLI |
Load GO -> gene associations from NCBI.
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| NcbiGeneLoaderCLI |
Command line interface to gene parsing and loading
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| OptionsUtils |
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| OrderVectorsByDesignCli |
Use to change the order of the values to match the experimental design.
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| ProcessedDataComputeCLI |
Prepare the "processed" expression data vectors, and can also do batch correction.
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| ProcessedDataDeleterCli |
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| ProtocolAdderCli |
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| ProtocolDeleterCli |
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| ProtocolListCli |
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| PrototypeScopeResolver |
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| PubMedLoaderCli |
Load PubMed files from XML files -- not used routinely!
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| PubMedSearcher |
Simple application to perform pubmed searches from a list of terms, and persist the results in the database.
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| RawDataDeleterCli |
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| RawExpressionDataWriterCli |
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| RefreshExperimentCli |
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| ReplaceDataCli |
Replace data in an existing data set.
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| RNASeqBatchInfoCli |
Deprecated.
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| RNASeqDataAddCli |
Designed to add count and/or RPKM data to a data set that has only meta-data.
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| SettingsCompletionSource |
Provide completion for all available Gemma settings.
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| ShellUtils |
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| SingleCellDataAggregateDeleterCli |
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| SingleCellDataAggregatorCli |
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| SingleCellDataDeleterCli |
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| SingleCellDataDownloaderCli |
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| SingleCellDataLoaderCli |
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| SingleCellDataTransformCli |
Transform various single-cell formats.
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| SingleCellDataWriterCli |
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| SingleCellSparsityMetricsUpdaterCli |
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| SplitExperimentCli |
Split an experiment into parts based on an experimental factor
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| SuppressBatchTaskSummaryWriter |
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| SVDCli |
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| SystemCliContext |
A context for the CLI based on System. |
| TaxonLoaderCli |
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| TextBatchTaskSummaryWriter |
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| TsvBatchTaskSummaryWriter |
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| UnifiedOntologyUpdaterCli |
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| UpdateDatabaseCli |
Update the database.
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| UpdateEe2AdCli |
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| UpdateEE2CCli |
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| UpdateGene2CsCli |
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| 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.
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| VectorMergingCli |
For experiments that used multiple array designs, merge the expression profiles
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