Class FindObsoleteTermsCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.apps.FindObsoleteTermsCli

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI

@Deprecated
public class FindObsoleteTermsCli
extends AbstractAuthenticatedCLI

Deprecated.

superseded by GET /admin/ontologies/obsolete-terms, which answers the same question from a running application and additionally reports the replacement each ontology asserts.

This command exists only because a CLI has to load the ontologies itself — hence the load.ontologies=false precondition below and the warm-up loop. A running Gemma already holds them.

Two things the endpoint does not carry over. Its Count column is always 1: checkForObsolete increments the count but is only reached inside the checkedUris guard, so no term can be counted twice. And it walks every characteristic in the corpus to answer a question about distinct URIs — the endpoint groups CHARACTERISTIC by URI instead and asks each one once.

Scheduled for removal once the correction path lands; see docs/design/OBSOLETE_TERM_CORRECTION.md.

Nested Class Summary

Nested classes/interfaces inherited from interface CLI

CLI.CommandGroup

Field Summary

Fields inherited from class AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
FindObsoleteTermsCli()	Deprecated.

Method Summary

Modifier and Type	Method	Description
protected void	doAuthenticatedWork()	Deprecated.
CLI.CommandGroup	getCommandGroup()	Deprecated. Obtain the command group for this CLI.
String	getCommandName()	Deprecated. A short memorable name for the command that can be used to locate this class.
String	getShortDesc()	Deprecated. Obtain a short description for this command explaining what it does.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Deprecated. Process command line options.

Methods inherited from class AbstractAuthenticatedCLI

afterPropertiesSet, doWork, setAuthenticateAnonymously, setEnvironment, setRequireLogin

Methods inherited from class AbstractCLI

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, buildOptions, executeCommand, getApplicationContext, getBatchTaskExecutor, getBatchTaskProgressReporter, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getPipelineJobReporter, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis

Methods inherited from class Object

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

Constructor Details

FindObsoleteTermsCli

public FindObsoleteTermsCli()

Deprecated.

Method Details

getCommandGroup

public CLI.CommandGroup getCommandGroup()

Deprecated.

Description copied from interface: CLI

Obtain the command group for this CLI.

Specified by:

getCommandGroup in interface CLI

Overrides:

getCommandGroup in class AbstractCLI

getShortDesc

public String getShortDesc()

Deprecated.

Description copied from interface: CLI

Obtain a short description for this command explaining what it does.

Specified by:

getShortDesc in interface CLI

Overrides:

getShortDesc in class AbstractCLI

processOptions

protected void processOptions(org.apache.commons.cli.CommandLine commandLine)

Deprecated.

Description copied from class: AbstractCLI

Process command line options.

Implement this to provide processing of options. It is called after AbstractCLI.buildOptions(Options) and right before AbstractCLI.doWork().

Overrides:

processOptions in class AbstractCLI

getCommandName

public String getCommandName()

Deprecated.

Description copied from interface: CLI

A short memorable name for the command that can be used to locate this class.

Specified by:

getCommandName in interface CLI

Overrides:

getCommandName in class AbstractCLI

Returns:

name; if null or blank, this will not be available as a shortcut command.

doAuthenticatedWork

protected void doAuthenticatedWork()
                            throws Exception

Deprecated.

Specified by:

doAuthenticatedWork in class AbstractAuthenticatedCLI

Throws:

Exception