Package ubic.gemma.core.apps
Class RefreshExperimentCli
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- All Implemented Interfaces:
org.springframework.beans.factory.InitializingBean
,CLI
public class RefreshExperimentCli extends ExpressionExperimentManipulatingCLI
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Nested Class Summary
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Nested classes/interfaces inherited from interface ubic.gemma.core.util.CLI
CLI.CommandGroup
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Field Summary
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Fields inherited from class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
auditEventService, auditTrailService, eeService, entityLocator, entityUrlBuilder
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Fields inherited from class ubic.gemma.core.util.AbstractAutoSeekingCLI
FORCE_OPTION
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Fields inherited from class ubic.gemma.core.util.AbstractCLI
ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS
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Constructor Summary
Constructors Constructor Description RefreshExperimentCli()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
buildExperimentOptions(org.apache.commons.cli.Options options)
String
getCommandName()
A short memorable name for the command that can be used to locate this class.String
getShortDesc()
Obtain a short description for this command explaining what it does.protected void
processExperimentOptions(org.apache.commons.cli.CommandLine commandLine)
protected void
processExpressionExperiment(ExpressionExperiment bas)
Process anExpressionExperiment
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Methods inherited from class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, isAbortOnError, noNeedToRun, preprocessBioAssaySets, processBioAssaySet, processBioAssaySets, processExpressionExperimentSubSet, processOptions, processOtherBioAssaySet, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, setAbortOnError, setDefaultToAll, setSingleExperimentMode, setUseReferencesIfPossible
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Methods inherited from class ubic.gemma.core.util.AbstractAutoSeekingCLI
addAutoOption, addAutoOption, addForceOption, addLimitingDateOption, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, setForce
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Methods inherited from class ubic.gemma.core.util.AbstractAuthenticatedCLI
afterPropertiesSet, createBatchTaskExecutorService, doWork, setRequireLogin
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Methods inherited from class ubic.gemma.core.util.AbstractCLI
abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getBatchTaskExecutor, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments
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Method Detail
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getCommandName
public String getCommandName()
Description copied from interface:CLI
A short memorable name for the command that can be used to locate this class.- Specified by:
getCommandName
in interfaceCLI
- Overrides:
getCommandName
in classAbstractCLI
- Returns:
- name; if null or blank, this will not be available as a shortcut command.
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getShortDesc
public String getShortDesc()
Description copied from interface:CLI
Obtain a short description for this command explaining what it does.- Specified by:
getShortDesc
in interfaceCLI
- Overrides:
getShortDesc
in classAbstractCLI
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buildExperimentOptions
protected void buildExperimentOptions(org.apache.commons.cli.Options options)
- Overrides:
buildExperimentOptions
in classExpressionExperimentManipulatingCLI
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processExperimentOptions
protected void processExperimentOptions(org.apache.commons.cli.CommandLine commandLine) throws org.apache.commons.cli.ParseException
- Overrides:
processExperimentOptions
in classExpressionExperimentManipulatingCLI
- Throws:
org.apache.commons.cli.ParseException
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processExpressionExperiment
protected void processExpressionExperiment(ExpressionExperiment bas)
Description copied from class:ExpressionExperimentManipulatingCLI
Process anExpressionExperiment
.- Overrides:
processExpressionExperiment
in classExpressionExperimentManipulatingCLI
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