Package org.incenp.obofoundry.uberon

Class BasePlugin

java.lang.Object
org.incenp.obofoundry.uberon.BasePlugin
All Implemented Interfaces:
org.obolibrary.robot.Command
Direct Known Subclasses:
InferenceDiffCommand, MergeEquivalentSetsCommand, MergeSpeciesCommand, SpeciesSubsetCommand
public abstract class BasePlugin extends Object implements org.obolibrary.robot.Command
Helper base class for ROBOT commands. This class is intended to serve as a base class for ROBOT commands, to avoid duplicating boilerplate across several commands. Subclasses should call the constructor with the desired name, description, and help message, add any option they need, and implement the performOperation(org.obolibrary.robot.CommandState,org.apache.commons.cli.CommandLine) method.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected org.apache.commons.cli.Options
    options
     

    Fields inherited from interface org.obolibrary.robot.Command

    global, missingFileError

  • Constructor Summary

    Constructors
    Modifier
    Constructor
    Description
    protected
    BasePlugin(String name, String description, String usage)
    Creates a new command.

  • Method Summary

    Modifier and Type
    Method
    Description
    org.obolibrary.robot.CommandState
    execute(org.obolibrary.robot.CommandState state, String[] args)
     
    String
    getDescription()
     
    protected org.obolibrary.robot.IOHelper
    getIOHelper()
     
    protected org.semanticweb.owlapi.model.IRI
    getIRI(String term, String field)
    Create an IRI from a user-specified source.
    String
    getName()
     
    org.apache.commons.cli.Options
    getOptions()
     
    String
    getUsage()
     
    void
    main(String[] args)
     
    abstract void
    performOperation(org.obolibrary.robot.CommandState state, org.apache.commons.cli.CommandLine line)
    Perform whatever operation the command is supposed to do.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • options

      protected org.apache.commons.cli.Options options

  • Constructor Details

    • BasePlugin

      protected BasePlugin(String name, String description, String usage)
      Creates a new command.
      Parameters:
      name - The command name, as it should be invoked on the command line.
      description - The description of the command that ROBOT will display.
      usage - The help message for the command.

  • Method Details

    • getName

      public String getName()
      Specified by:
      getName in interface org.obolibrary.robot.Command

    • getDescription

      public String getDescription()
      Specified by:
      getDescription in interface org.obolibrary.robot.Command

    • getUsage

      public String getUsage()
      Specified by:
      getUsage in interface org.obolibrary.robot.Command

    • getOptions

      public org.apache.commons.cli.Options getOptions()
      Specified by:
      getOptions in interface org.obolibrary.robot.Command

    • main

      public void main(String[] args)
      Specified by:
      main in interface org.obolibrary.robot.Command

    • execute

      public org.obolibrary.robot.CommandState execute(org.obolibrary.robot.CommandState state, String[] args) throws Exception
      Specified by:
      execute in interface org.obolibrary.robot.Command
      Throws:
      Exception

    • performOperation

      public abstract void performOperation(org.obolibrary.robot.CommandState state, org.apache.commons.cli.CommandLine line) throws Exception
      Perform whatever operation the command is supposed to do.
      Parameters:
      state - The internal state of ROBOT.
      line - The command line used to invoke the command.
      Throws:
      Exception - If any error occurred when attempting to execute the operation.

    • getIRI

      protected org.semanticweb.owlapi.model.IRI getIRI(String term, String field)
      Create an IRI from a user-specified source. This delegates the task of expanding CURIEs to ROBOT, which may use whatever informations it has (such as prefix mappings specified using the --prefix option).
      Parameters:
      term - the term to transform into an IRI.
      field - The source where the term comes from. Used in ROBOT's error message, if the term cannot be transformed into an IRI.
      Returns:
      The resulting IRI.

    • getIOHelper

      protected org.obolibrary.robot.IOHelper getIOHelper()