Package ubic.gemma.core.util

Class AbstractAuthenticatedCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

All Implemented Interfaces:

CLI

Direct Known Subclasses:

ArrayDesignAlternativePopulateCli, ArrayDesignSequenceManipulatingCli, BibRefUpdaterCli, BlacklistCli, DatabaseViewGeneratorCLI, DeleteEvidenceCLI, EvidenceImporterAbstractCLI, ExperimentalDesignImportCli, ExperimentalDesignViewCli, ExpressionExperimentManipulatingCLI, ExternalDatabaseAdderCli, ExternalDatabaseEvidenceImporterAbstractCLI, ExternalDatabaseOverviewCli, ExternalDatabaseUpdaterCli, ExternalFileGeneLoaderCLI, FactorValueMigratorCLI, GenericGenelistDesignGenerator, GeoGrabberCli, LoadEvidenceForClassifier, LoadExpressionDataCli, LoadSimpleExpressionDataCli, MultifunctionalityCli, NCBIGene2GOAssociationLoaderCLI, NcbiGeneLoaderCLI, PubMedLoaderCli, PubMedSearcher, TaxonLoaderCli, UpdatePubMedCli

public abstract class AbstractAuthenticatedCLI
extends AbstractCLI

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

Credentials may be supplied via the environment using the $GEMMMA_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).

Author:

pavlidis

Field Summary

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

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
AbstractAuthenticatedCLI()

Method Summary

Modifier and Type	Method	Description
protected <T> List<T>	executeBatchTasks(Collection<? extends Callable<T>> tasks)	Execute batch tasks using a preconfigured ExecutorService and return all the resulting tasks results.
protected void	processStandardOptions(org.apache.commons.cli.CommandLine commandLine)	You must override this method to process any options you added.
protected boolean	requireLogin()	Indicate if the command requires authentication.

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

addAutoOption, addAutoOption, addBatchOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, buildOptions, buildStandardOptions, doWork, executeCommand, getAutoSeekEventType, getBean, getBean, getLimitingDate, getNumThreads, getOptions, isAutoSeek, processOptions, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.util.CLI

getCommandGroup, getCommandName, getShortDesc

Constructor Detail

AbstractAuthenticatedCLI

public AbstractAuthenticatedCLI()

Method Detail

requireLogin

protected boolean requireLogin()

Indicate if the command requires authentication.

Override this to return true to make authentication required.

Returns:

true if login is required, otherwise false

processStandardOptions

protected void processStandardOptions(org.apache.commons.cli.CommandLine commandLine)
                               throws org.apache.commons.cli.ParseException

You must override this method to process any options you added.

Overrides:

processStandardOptions in class AbstractCLI

Throws:

org.apache.commons.cli.ParseException

executeBatchTasks

protected <T> List<T> executeBatchTasks(Collection<? extends Callable<T>> tasks)
                                 throws InterruptedException

Execute batch tasks using a preconfigured ExecutorService and return all the resulting tasks results.

Tasks are wrapped with DelegatingSecurityContextCallable to ensure that they execute with the security context set up by authenticate().

Overrides:

executeBatchTasks in class AbstractCLI

Throws:

InterruptedException