Package org.incenp.obofoundry.odk

Class ObsoleteReplaceCommand

java.lang.Object

org.incenp.obofoundry.odk.BasePlugin

org.incenp.obofoundry.odk.ObsoleteReplaceCommand

All Implemented Interfaces:

org.obolibrary.robot.Command

public class ObsoleteReplaceCommand
extends BasePlugin

A command to obsolete an entity and replace all its usages with a replacement entity.

This command takes an entity to obsolete and a replacement entity. It will:

• Replace all usages of the obsolete entity with the replacement entity throughout the ontology
• Remove the label, comment, and definition from the obsolete entity
• Mark the obsolete entity as deprecated
• Add a new label prefixed with "obsolete" to the obsolete entity
• Add the original label of the obsolete entity as an exact synonym on the replacement entity (with a dbxref annotation pointing to the obsolete entity)
• Add a "term replaced by" annotation on the obsolete entity pointing to the replacement entity

Field Summary

Fields inherited from class org.incenp.obofoundry.odk.BasePlugin

ioHelper, options

Fields inherited from interface org.obolibrary.robot.Command

global, missingFileError

Constructor Summary

Constructors

Constructor	Description
ObsoleteReplaceCommand()

Method Summary

Modifier and Type	Method	Description
void	performOperation(org.obolibrary.robot.CommandState state, org.apache.commons.cli.CommandLine line)	Performs whatever operation the command is supposed to do.

Methods inherited from class org.incenp.obofoundry.odk.BasePlugin

execute, getDescription, getIRI, getName, getOptions, getUsage, main

Methods inherited from class java.lang.Object

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

Constructor Details

ObsoleteReplaceCommand

public ObsoleteReplaceCommand()

Method Details

performOperation

public void performOperation(org.obolibrary.robot.CommandState state,
 org.apache.commons.cli.CommandLine line)
                      throws Exception

Description copied from class: BasePlugin

Performs whatever operation the command is supposed to do.

Specified by:

performOperation in class BasePlugin

Parameters:

state - The internal state of ROBOT.

line - The command line used to invoke the command.

Throws:

Exception - If any error occurs when attempting to execute the operation.