Package ubic.gemma.core.util

Class AbstractAuthenticatedCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, CLI

Direct Known Subclasses:

AbstractAutoSeekingCLI, AbstractCrudCli, ArrayDesignAlternativePopulateCli, BibRefUpdaterCli, BlacklistCli, DatabaseViewGeneratorCLI, ExperimentalDesignViewCli, ExternalDatabaseAdderCli, ExternalDatabaseOverviewCli, ExternalDatabaseUpdaterCli, ExternalFileGeneLoaderCLI, FactorValueMigratorCLI, FindObsoleteTermsCli, FixOntologyTermLabelsCli, GenericGenelistDesignGenerator, GeoGrabberCli, LoadExpressionDataCli, LoadSimpleExpressionDataCli, MultifunctionalityCli, NCBIGene2GOAssociationLoaderCLI, NcbiGeneLoaderCLI, ProtocolAdderCli, ProtocolDeleterCli, ProtocolListCli, PubMedLoaderCli, PubMedSearcher, TaxonLoaderCli, UpdateEe2AdCli, UpdateEE2CCli, UpdateGene2CsCli, UpdatePubMedCli

public abstract class AbstractAuthenticatedCLI
extends AbstractCLI
implements org.springframework.beans.factory.InitializingBean

Subclass this to create command line interface (CLI) tools that need authentication.

Credentials may be supplied via the environment using the $GEMMA_USERNAME and $GEMMA_PASSWORD variables. A more secure $GEMMA_PASSWORD_CMD variable can be used to specify a command that produces the password. If no environment variables are supplied, they will be prompted if the standard input is attached to a console (i.e tty).

If the test or testdb profile is active, environment variables with the $GEMMA_TEST_DB_ prefix will be looked up instead.

Author:

pavlidis

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.util.CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ubic.gemma.core.util.AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
AbstractAuthenticatedCLI()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
protected ExecutorService	createBatchTaskExecutorService()	Create an ExecutorService to be used for running batch tasks.
protected abstract void	doAuthenticatedWork()
protected void	doWork()	Command line implementation.
protected void	setRequireLogin()	Indicate that the command requires authentication.

Methods inherited from class ubic.gemma.core.util.AbstractCLI

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, awaitBatchExecutorService, buildOptions, executeCommand, getBatchTaskExecutor, getCliContext, getCommandAliases, getCommandGroup, getCommandName, getHelpFooter, getNumThreads, getOptions, getShortDesc, getUsage, processOptions, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractAuthenticatedCLI

public AbstractAuthenticatedCLI()

Method Detail

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

Throws:

Exception

setRequireLogin

protected void setRequireLogin()

Indicate that the command requires authentication.

doWork

protected final void doWork()
                     throws Exception

Description copied from class: AbstractCLI

Command line implementation.

This is called after AbstractCLI.buildOptions(Options) and AbstractCLI.processOptions(CommandLine). so the implementation can assume that all its arguments have already been initialized and any setup behaviour have been performed.

Specified by:

doWork in class AbstractCLI

Throws:

Exception - in case of unrecoverable failure, an exception is thrown and will result in a AbstractCLI.FAILURE exit code, otherwise use AbstractCLI.addErrorObject(java.lang.Object, java.lang.String, java.lang.Throwable) to indicate an error and resume processing

doAuthenticatedWork

protected abstract void doAuthenticatedWork()
                                     throws Exception

Throws:

Exception

createBatchTaskExecutorService

protected ExecutorService createBatchTaskExecutorService()

Description copied from class: AbstractCLI

Create an ExecutorService to be used for running batch tasks.

Overrides:

createBatchTaskExecutorService in class AbstractCLI